diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0535814391..12ed40b678 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -208,6 +208,7 @@ jobs: - tags: "fastp" - tags: "fastqc" - tags: "samtools/stats" + - tags: "untar" env: NXF_ANSI_LOG: false TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" diff --git a/CHANGELOG.md b/CHANGELOG.md index bd6bd0ac47..b686bd5ed7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,8 @@ Pårtetjåkko is a mountain in the south of the park. - [#1244](https://github.com/nf-core/sarek/pull/1244) - Add bcf annotate module - [#1252](https://github.com/nf-core/sarek/pull/1252) - Added NGSCheckMate tool for checking that samples come from the same individual - [#1271](https://github.com/nf-core/sarek/pull/1271) - Back to dev -- [#1290](https://github.com/nf-core/sarek/pull/1290) - Add nf-test for whole pipeline. +- [#1288](https://github.com/nf-core/sarek/pull/1288) - Add nf-test continuous integration (but no tests) +- [#1290](https://github.com/nf-core/sarek/pull/1290) - Add nf-test for whole pipeline ### Changed @@ -28,6 +29,7 @@ Pårtetjåkko is a mountain in the south of the park. - [#1317](https://github.com/nf-core/sarek/pull/1317) - Add new tools to subway map - [#1325](https://github.com/nf-core/sarek/pull/1325) - Move `sentieon_dnascope_model` params into `igenomes.config` - [#1325](https://github.com/nf-core/sarek/pull/1325) - Refactor config files +- [#1327](https://github.com/nf-core/sarek/pull/1327) - Update modules to have an conda environment name ### Fixed @@ -39,6 +41,8 @@ Pårtetjåkko is a mountain in the south of the park. - [#1318](https://github.com/nf-core/sarek/pull/1218) - Fix writing of params.json on S3 - [#1324](https://github.com/nf-core/sarek/pull/1324) - Fix various typos & code formatting - [#1325](https://github.com/nf-core/sarek/pull/1325) - Update bcfannotate tests and related config files +- [#1328](https://github.com/nf-core/sarek/pull/1328) - Fix links to docs in `nextflow_schema.json` and `docs/output.md` +- [#1328](https://github.com/nf-core/sarek/pull/1328) - Add missing icons in `nextflow_schema.json` - [#1330](https://github.com/nf-core/sarek/pull/1330) - Add SnpEff to full sized tests ### Removed diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config index 9cf5be71d4..ff046ca843 100644 --- a/conf/modules/annotate.config +++ b/conf/modules/annotate.config @@ -37,7 +37,7 @@ process { ext.args = { [ (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', - (params.vep_loftee) ? "--plugin LoF,loftee_path://usr/local/share/ensembl-vep-${params.vep_version}" : '', + (params.vep_loftee) ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '', (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '', (params.vep_spliceregion) ? '--plugin SpliceRegion' : '', (params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf', diff --git a/docs/output.md b/docs/output.md index 769ee71fbd..ff6445e89b 100644 --- a/docs/output.md +++ b/docs/output.md @@ -315,7 +315,7 @@ If some results from a variant caller do not appear here, please check out the ` ### SNVs and small indels -For single nucleotide variants (SNVs) and small indels, multiple tools are available for normal (germline), tumor-only, and tumor-normal (somatic) paired data. For a list of the appropriate tool(s) for the data and sequencing type at hand, please check [here](usage.md#which-tool). +For single nucleotide variants (SNVs) and small indels, multiple tools are available for normal (germline), tumor-only, and tumor-normal (somatic) paired data. For a list of the appropriate tool(s) for the data and sequencing type at hand, please check [here](usage#which-tool). #### bcftools diff --git a/modules.json b/modules.json index 7fd7d8eeb0..dd5387fbb8 100644 --- a/modules.json +++ b/modules.json @@ -7,481 +7,481 @@ "nf-core": { "ascat": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "bcftools/annotate": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "bcftools/mpileup": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["bam_ngscheckmate"] }, "bcftools/sort": { "branch": "master", - 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"git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", + "git_sha": "214d575774c172062924ad3564b4f66655600730", "installed_by": ["modules"] }, "sentieon/haplotyper": { "branch": "master", - "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "sentieon/varcal": { "branch": "master", - "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "snpeff/download": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "214d575774c172062924ad3564b4f66655600730", "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["vcf_annotate_snpeff", "modules"] + "git_sha": "214d575774c172062924ad3564b4f66655600730", + "installed_by": ["modules", "vcf_annotate_snpeff"] }, "strelka/germline": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "strelka/somatic": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "svdb/merge": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["vcf_annotate_snpeff", "modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": ["modules", "vcf_annotate_snpeff"] }, "tabix/tabix": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["vcf_annotate_ensemblvep", "modules"] }, "tiddit/sv": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "unzip": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "vcftools": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] } } diff --git a/modules/local/add_info_to_vcf/environment.yml b/modules/local/add_info_to_vcf/environment.yml index 710fbfd120..34513c7f4a 100644 --- a/modules/local/add_info_to_vcf/environment.yml +++ b/modules/local/add_info_to_vcf/environment.yml @@ -1,3 +1,4 @@ +name: gawk channels: - conda-forge - bioconda diff --git a/modules/local/build_intervals/environment.yml b/modules/local/build_intervals/environment.yml index 710fbfd120..34513c7f4a 100644 --- a/modules/local/build_intervals/environment.yml +++ b/modules/local/build_intervals/environment.yml @@ -1,3 +1,4 @@ +name: gawk channels: - conda-forge - bioconda diff --git a/modules/local/create_intervals_bed/environment.yml b/modules/local/create_intervals_bed/environment.yml index 710fbfd120..34513c7f4a 100644 --- a/modules/local/create_intervals_bed/environment.yml +++ b/modules/local/create_intervals_bed/environment.yml @@ -1,3 +1,4 @@ +name: gawk channels: - conda-forge - bioconda diff --git a/modules/nf-core/ascat/environment.yml b/modules/nf-core/ascat/environment.yml index 6708ce86a8..52935f0978 100644 --- a/modules/nf-core/ascat/environment.yml +++ b/modules/nf-core/ascat/environment.yml @@ -1,3 +1,4 @@ +name: ascat channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml index 57631f42ea..273ffff4c2 100644 --- a/modules/nf-core/bcftools/annotate/environment.yml +++ b/modules/nf-core/bcftools/annotate/environment.yml @@ -1,3 +1,4 @@ +name: bcftools_annotate channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml index 57631f42ea..be2539990b 100644 --- a/modules/nf-core/bcftools/concat/environment.yml +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -1,3 +1,4 @@ +name: bcftools_concat channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/mpileup/environment.yml b/modules/nf-core/bcftools/mpileup/environment.yml index 57631f42ea..346d187fec 100644 --- a/modules/nf-core/bcftools/mpileup/environment.yml +++ b/modules/nf-core/bcftools/mpileup/environment.yml @@ -1,3 +1,4 @@ +name: bcftools_mpileup channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml index 57631f42ea..26d3644501 100644 --- a/modules/nf-core/bcftools/sort/environment.yml +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -1,3 +1,4 @@ +name: bcftools_sort channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml index 57631f42ea..a937a10a7f 100644 --- a/modules/nf-core/bcftools/stats/environment.yml +++ b/modules/nf-core/bcftools/stats/environment.yml @@ -1,3 +1,4 @@ +name: bcftools_stats channels: - conda-forge - bioconda diff --git a/modules/nf-core/bwa/index/environment.yml b/modules/nf-core/bwa/index/environment.yml index c5b0826008..5d3cb3231b 100644 --- a/modules/nf-core/bwa/index/environment.yml +++ b/modules/nf-core/bwa/index/environment.yml @@ -1,3 +1,4 @@ +name: bwa_index channels: - conda-forge - bioconda diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml index 34f50c48b4..401a0d06ce 100644 --- a/modules/nf-core/bwa/mem/environment.yml +++ b/modules/nf-core/bwa/mem/environment.yml @@ -1,7 +1,9 @@ +name: bwa_mem channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::bwa=0.7.17 - - bioconda::samtools=1.16.1 + - bwa=0.7.17 + # renovate: datasource=conda depName=bioconda/samtools + - samtools=1.16.1 diff --git a/modules/nf-core/bwamem2/index/environment.yml b/modules/nf-core/bwamem2/index/environment.yml index cef9ec4e78..26b439172a 100644 --- a/modules/nf-core/bwamem2/index/environment.yml +++ b/modules/nf-core/bwamem2/index/environment.yml @@ -1,3 +1,4 @@ +name: bwamem2_index channels: - conda-forge - bioconda diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml index 2d75270b2b..67989071e3 100644 --- a/modules/nf-core/bwamem2/mem/environment.yml +++ b/modules/nf-core/bwamem2/mem/environment.yml @@ -1,7 +1,9 @@ +name: bwamem2_mem channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::bwa-mem2=2.2.1 - - bioconda::samtools=1.16.1 + - bwa-mem2=2.2.1 + # renovate: datasource=conda depName=bioconda/samtools + - samtools=1.16.1 diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml index cdad6baafc..17a04ef232 100644 --- a/modules/nf-core/cat/cat/environment.yml +++ b/modules/nf-core/cat/cat/environment.yml @@ -1,3 +1,4 @@ +name: cat_cat channels: - conda-forge - bioconda diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index 222b301f38..bff93add01 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -1,3 +1,4 @@ +name: cat_fastq channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvkit/antitarget/environment.yml b/modules/nf-core/cnvkit/antitarget/environment.yml index ef6bec487e..08a0b27cea 100644 --- a/modules/nf-core/cnvkit/antitarget/environment.yml +++ b/modules/nf-core/cnvkit/antitarget/environment.yml @@ -1,3 +1,4 @@ +name: cnvkit_antitarget channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvkit/batch/environment.yml b/modules/nf-core/cnvkit/batch/environment.yml index ef6bec487e..eb9ed375b7 100644 --- a/modules/nf-core/cnvkit/batch/environment.yml +++ b/modules/nf-core/cnvkit/batch/environment.yml @@ -1,3 +1,4 @@ +name: cnvkit_batch channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvkit/genemetrics/environment.yml b/modules/nf-core/cnvkit/genemetrics/environment.yml index ef6bec487e..2d00f762e2 100644 --- a/modules/nf-core/cnvkit/genemetrics/environment.yml +++ b/modules/nf-core/cnvkit/genemetrics/environment.yml @@ -1,3 +1,4 @@ +name: cnvkit_genemetrics channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvkit/reference/environment.yml b/modules/nf-core/cnvkit/reference/environment.yml index ef6bec487e..6bb62f9054 100644 --- a/modules/nf-core/cnvkit/reference/environment.yml +++ b/modules/nf-core/cnvkit/reference/environment.yml @@ -1,3 +1,4 @@ +name: cnvkit_reference channels: - conda-forge - bioconda diff --git a/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff b/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff index c8ace426e4..c8dc392666 100644 --- a/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff +++ b/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff @@ -1,4 +1,13 @@ Changes in module 'nf-core/controlfreec/assesssignificance' +--- modules/nf-core/controlfreec/assesssignificance/environment.yml ++++ modules/nf-core/controlfreec/assesssignificance/environment.yml +@@ -4,4 +4,4 @@ + - bioconda + - defaults + dependencies: +- - bioconda::control-freec=11.6b ++ - bioconda::control-freec=11.6 + --- modules/nf-core/controlfreec/assesssignificance/main.nf +++ modules/nf-core/controlfreec/assesssignificance/main.nf @@ -4,8 +4,8 @@ @@ -13,13 +22,4 @@ Changes in module 'nf-core/controlfreec/assesssignificance' input: tuple val(meta), path(cnvs), path(ratio) ---- modules/nf-core/controlfreec/assesssignificance/environment.yml -+++ modules/nf-core/controlfreec/assesssignificance/environment.yml -@@ -3,4 +3,4 @@ - - bioconda - - defaults - dependencies: -- - bioconda::control-freec=11.6b -+ - bioconda::control-freec=11.6 - ************************************************************ diff --git a/modules/nf-core/controlfreec/assesssignificance/environment.yml b/modules/nf-core/controlfreec/assesssignificance/environment.yml index f1047dbbbb..cb0b9c17c3 100644 --- a/modules/nf-core/controlfreec/assesssignificance/environment.yml +++ b/modules/nf-core/controlfreec/assesssignificance/environment.yml @@ -1,3 +1,4 @@ +name: controlfreec_assesssignificance channels: - conda-forge - bioconda diff --git a/modules/nf-core/controlfreec/freec/environment.yml b/modules/nf-core/controlfreec/freec/environment.yml index 83094f46ca..cb76c6ba93 100644 --- a/modules/nf-core/controlfreec/freec/environment.yml +++ b/modules/nf-core/controlfreec/freec/environment.yml @@ -1,3 +1,4 @@ +name: controlfreec_freec channels: - conda-forge - bioconda diff --git a/modules/nf-core/controlfreec/freec2bed/environment.yml b/modules/nf-core/controlfreec/freec2bed/environment.yml index 83094f46ca..12601ffa55 100644 --- a/modules/nf-core/controlfreec/freec2bed/environment.yml +++ b/modules/nf-core/controlfreec/freec2bed/environment.yml @@ -1,3 +1,4 @@ +name: controlfreec_freec2bed channels: - conda-forge - bioconda diff --git a/modules/nf-core/controlfreec/freec2circos/environment.yml b/modules/nf-core/controlfreec/freec2circos/environment.yml index 83094f46ca..1915abfd7f 100644 --- a/modules/nf-core/controlfreec/freec2circos/environment.yml +++ b/modules/nf-core/controlfreec/freec2circos/environment.yml @@ -1,3 +1,4 @@ +name: controlfreec_freec2circos channels: - conda-forge - bioconda diff --git a/modules/nf-core/controlfreec/makegraph/environment.yml b/modules/nf-core/controlfreec/makegraph/environment.yml index 83094f46ca..897eadf3bd 100644 --- a/modules/nf-core/controlfreec/makegraph/environment.yml +++ b/modules/nf-core/controlfreec/makegraph/environment.yml @@ -1,3 +1,4 @@ +name: controlfreec_makegraph channels: - conda-forge - bioconda diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index 9d0e6b2090..f0c63f6984 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -1,3 +1,4 @@ +name: custom_dumpsoftwareversions channels: - conda-forge - bioconda diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index 9414c32d71..5f15a5fde0 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: diff --git a/modules/nf-core/deepvariant/environment.yml b/modules/nf-core/deepvariant/environment.yml index bcd3a8b1c6..648a76dea6 100644 --- a/modules/nf-core/deepvariant/environment.yml +++ b/modules/nf-core/deepvariant/environment.yml @@ -1,3 +1,4 @@ +name: deepvariant channels: - conda-forge - bioconda diff --git a/modules/nf-core/dragmap/align/environment.yml b/modules/nf-core/dragmap/align/environment.yml index 66482a4f9f..b00e62f435 100644 --- a/modules/nf-core/dragmap/align/environment.yml +++ b/modules/nf-core/dragmap/align/environment.yml @@ -1,8 +1,10 @@ +name: dragmap_align channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::dragmap=1.2.1 - - bioconda::samtools=1.15.1 - - conda-forge::pigz=2.3.4 + - dragmap=1.2.1 + # renovate: datasource=conda depName=bioconda/samtools + - samtools=1.15.1 + - pigz=2.3.4 diff --git a/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff b/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff index aeb9694244..a5823ce8bc 100644 --- a/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff +++ b/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff @@ -1,4 +1,13 @@ Changes in module 'nf-core/dragmap/hashtable' +--- modules/nf-core/dragmap/hashtable/environment.yml ++++ modules/nf-core/dragmap/hashtable/environment.yml +@@ -4,4 +4,4 @@ + - bioconda + - defaults + dependencies: +- - bioconda::dragmap=1.3.0 ++ - bioconda::dragmap=1.2.1 + --- modules/nf-core/dragmap/hashtable/main.nf +++ modules/nf-core/dragmap/hashtable/main.nf @@ -4,8 +4,8 @@ @@ -13,13 +22,4 @@ Changes in module 'nf-core/dragmap/hashtable' input: tuple val(meta), path(fasta) ---- modules/nf-core/dragmap/hashtable/environment.yml -+++ modules/nf-core/dragmap/hashtable/environment.yml -@@ -3,4 +3,4 @@ - - bioconda - - defaults - dependencies: -- - bioconda::dragmap=1.3.0 -+ - bioconda::dragmap=1.2.1 - ************************************************************ diff --git a/modules/nf-core/dragmap/hashtable/environment.yml b/modules/nf-core/dragmap/hashtable/environment.yml index c8e351255f..3c3d1404f4 100644 --- a/modules/nf-core/dragmap/hashtable/environment.yml +++ b/modules/nf-core/dragmap/hashtable/environment.yml @@ -1,3 +1,4 @@ +name: dragmap_hashtable channels: - conda-forge - bioconda diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml index d3805c0c05..beebaca634 100644 --- a/modules/nf-core/ensemblvep/download/environment.yml +++ b/modules/nf-core/ensemblvep/download/environment.yml @@ -1,3 +1,4 @@ +name: ensemblvep_download channels: - conda-forge - bioconda diff --git a/modules/nf-core/ensemblvep/download/meta.yml b/modules/nf-core/ensemblvep/download/meta.yml index 0183a435b8..a4277ad7a7 100644 --- a/modules/nf-core/ensemblvep/download/meta.yml +++ b/modules/nf-core/ensemblvep/download/meta.yml @@ -1,4 +1,4 @@ -name: ENSEMBLVEP_DOWNLOAD +name: ensemblvep_download description: Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through `task.ext.args`. keywords: - annotation diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index d3805c0c05..7a12774608 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -1,3 +1,4 @@ +name: ensemblvep_vep channels: - conda-forge - bioconda diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index 61d29d3fb1..d8ff8d1443 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -1,4 +1,4 @@ -name: ENSEMBLVEP_VEP +name: ensemblvep_vep description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. keywords: - annotation diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index 19ccec2564..70389e664c 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -1,3 +1,4 @@ +name: fastp channels: - conda-forge - bioconda diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index f52a53a0fa..1787b38a9a 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,3 +1,4 @@ +name: fastqc channels: - conda-forge - bioconda diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml b/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml index d64c6844b3..1429e478ec 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml @@ -1,3 +1,4 @@ +name: fgbio_callmolecularconsensusreads channels: - conda-forge - bioconda diff --git a/modules/nf-core/fgbio/fastqtobam/environment.yml b/modules/nf-core/fgbio/fastqtobam/environment.yml index d64c6844b3..f5f1992581 100644 --- a/modules/nf-core/fgbio/fastqtobam/environment.yml +++ b/modules/nf-core/fgbio/fastqtobam/environment.yml @@ -1,3 +1,4 @@ +name: fgbio_fastqtobam channels: - conda-forge - bioconda diff --git a/modules/nf-core/fgbio/groupreadsbyumi/environment.yml b/modules/nf-core/fgbio/groupreadsbyumi/environment.yml index d64c6844b3..58e37bf6bd 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/environment.yml +++ b/modules/nf-core/fgbio/groupreadsbyumi/environment.yml @@ -1,3 +1,4 @@ +name: fgbio_groupreadsbyumi channels: - conda-forge - bioconda diff --git a/modules/nf-core/freebayes/environment.yml b/modules/nf-core/freebayes/environment.yml index b074f213f4..6846080a2f 100644 --- a/modules/nf-core/freebayes/environment.yml +++ b/modules/nf-core/freebayes/environment.yml @@ -1,3 +1,4 @@ +name: freebayes channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index 16241b6d94..a690099123 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_applybqsr channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/applyvqsr/environment.yml b/modules/nf-core/gatk4/applyvqsr/environment.yml index 16241b6d94..e640768957 100644 --- a/modules/nf-core/gatk4/applyvqsr/environment.yml +++ b/modules/nf-core/gatk4/applyvqsr/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_applyvqsr channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index 16241b6d94..6863fb1712 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_baserecalibrator channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml index 16241b6d94..d5e45ebe42 100644 --- a/modules/nf-core/gatk4/calculatecontamination/environment.yml +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_calculatecontamination channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/cnnscorevariants/environment.yml b/modules/nf-core/gatk4/cnnscorevariants/environment.yml index bcd3a8b1c6..12cc34ba66 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/environment.yml +++ b/modules/nf-core/gatk4/cnnscorevariants/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_cnnscorevariants channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index 16241b6d94..db663e148f 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_createsequencedictionary channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml index 16241b6d94..fabb6f2ba4 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_estimatelibrarycomplexity channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml index 16241b6d94..8057d765d5 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/environment.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_filtermutectcalls channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml index 16241b6d94..faeea8ddb0 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/environment.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_filtervarianttranches channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml index 16241b6d94..928ac76e6b 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_gatherbqsrreports channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml index 16241b6d94..1a2ebf5761 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_gatherpileupsummaries channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml index 16241b6d94..ce3f941694 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/environment.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_genomicsdbimport channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml index 16241b6d94..49f213790d 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/environment.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_genotypegvcfs channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml index 16241b6d94..d650467cf8 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_getpileupsummaries channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index 16241b6d94..0c8f32fa63 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_haplotypecaller channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/intervallisttobed/environment.yml b/modules/nf-core/gatk4/intervallisttobed/environment.yml index 16241b6d94..06d9f0e9c7 100644 --- a/modules/nf-core/gatk4/intervallisttobed/environment.yml +++ b/modules/nf-core/gatk4/intervallisttobed/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_intervallisttobed channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml index 16241b6d94..d1c35caf83 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_learnreadorientationmodel channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index 8c0c6bb279..9adad104d8 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_markduplicates channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/mergemutectstats/environment.yml b/modules/nf-core/gatk4/mergemutectstats/environment.yml index 16241b6d94..dd132c3a3d 100644 --- a/modules/nf-core/gatk4/mergemutectstats/environment.yml +++ b/modules/nf-core/gatk4/mergemutectstats/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_mergemutectstats channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index 16241b6d94..d6c3e51a9f 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_mergevcfs channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/mutect2/environment.yml b/modules/nf-core/gatk4/mutect2/environment.yml index 16241b6d94..54da66ce57 100644 --- a/modules/nf-core/gatk4/mutect2/environment.yml +++ b/modules/nf-core/gatk4/mutect2/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_mutect2 channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/variantrecalibrator/environment.yml b/modules/nf-core/gatk4/variantrecalibrator/environment.yml index 16241b6d94..619208a56d 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/environment.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_variantrecalibrator channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4spark/applybqsr/environment.yml b/modules/nf-core/gatk4spark/applybqsr/environment.yml index 821728a662..709dd488c9 100644 --- a/modules/nf-core/gatk4spark/applybqsr/environment.yml +++ b/modules/nf-core/gatk4spark/applybqsr/environment.yml @@ -1,3 +1,4 @@ +name: gatk4spark_applybqsr channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml index 821728a662..bf2568a2a8 100644 --- a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml @@ -1,3 +1,4 @@ +name: gatk4spark_baserecalibrator channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4spark/markduplicates/environment.yml b/modules/nf-core/gatk4spark/markduplicates/environment.yml index 821728a662..3e33d7fe3d 100644 --- a/modules/nf-core/gatk4spark/markduplicates/environment.yml +++ b/modules/nf-core/gatk4spark/markduplicates/environment.yml @@ -1,3 +1,4 @@ +name: gatk4spark_markduplicates channels: - conda-forge - bioconda diff --git a/modules/nf-core/manta/germline/environment.yml b/modules/nf-core/manta/germline/environment.yml index 235b1ba75d..4a63d3084b 100644 --- a/modules/nf-core/manta/germline/environment.yml +++ b/modules/nf-core/manta/germline/environment.yml @@ -1,3 +1,4 @@ +name: manta_germline channels: - conda-forge - bioconda diff --git a/modules/nf-core/manta/somatic/environment.yml b/modules/nf-core/manta/somatic/environment.yml index 235b1ba75d..aac8827dfc 100644 --- a/modules/nf-core/manta/somatic/environment.yml +++ b/modules/nf-core/manta/somatic/environment.yml @@ -1,3 +1,4 @@ +name: manta_somatic channels: - conda-forge - bioconda diff --git a/modules/nf-core/manta/tumoronly/environment.yml b/modules/nf-core/manta/tumoronly/environment.yml index 235b1ba75d..cf5db361e0 100644 --- a/modules/nf-core/manta/tumoronly/environment.yml +++ b/modules/nf-core/manta/tumoronly/environment.yml @@ -1,3 +1,4 @@ +name: manta_tumoronly channels: - conda-forge - bioconda diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index f1521e08a2..b12e3cb127 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -1,6 +1,8 @@ +name: mosdepth channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::mosdepth=0.3.3 + # renovate: datasource=conda depName=bioconda/mosdepth + - mosdepth=0.3.3 diff --git a/modules/nf-core/msisensorpro/msisomatic/environment.yml b/modules/nf-core/msisensorpro/msisomatic/environment.yml index 6d85f22481..147a9d6b85 100644 --- a/modules/nf-core/msisensorpro/msisomatic/environment.yml +++ b/modules/nf-core/msisensorpro/msisomatic/environment.yml @@ -1,3 +1,4 @@ +name: msisensorpro_msisomatic channels: - conda-forge - bioconda diff --git a/modules/nf-core/msisensorpro/scan/environment.yml b/modules/nf-core/msisensorpro/scan/environment.yml index 6d85f22481..377c28a61b 100644 --- a/modules/nf-core/msisensorpro/scan/environment.yml +++ b/modules/nf-core/msisensorpro/scan/environment.yml @@ -1,3 +1,4 @@ +name: msisensorpro_scan channels: - conda-forge - bioconda diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 9d0e6b2090..d2a9f21a74 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,3 +1,4 @@ +name: multiqc channels: - conda-forge - bioconda diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index a61223ed7a..f1aa660eb7 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,5 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: MultiQC +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC diff --git a/modules/nf-core/ngscheckmate/ncm/environment.yml b/modules/nf-core/ngscheckmate/ncm/environment.yml index fde8331fad..bf185fc23e 100644 --- a/modules/nf-core/ngscheckmate/ncm/environment.yml +++ b/modules/nf-core/ngscheckmate/ncm/environment.yml @@ -1,3 +1,4 @@ +name: ngscheckmate_ncm channels: - conda-forge - bioconda diff --git a/modules/nf-core/samblaster/environment.yml b/modules/nf-core/samblaster/environment.yml index 3a79aaf8ea..f956283ec0 100644 --- a/modules/nf-core/samblaster/environment.yml +++ b/modules/nf-core/samblaster/environment.yml @@ -1,3 +1,4 @@ +name: samblaster channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/bam2fq/environment.yml b/modules/nf-core/samtools/bam2fq/environment.yml index 04c82f1423..b59ea8e050 100644 --- a/modules/nf-core/samtools/bam2fq/environment.yml +++ b/modules/nf-core/samtools/bam2fq/environment.yml @@ -1,3 +1,4 @@ +name: samtools_bam2fq channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/collatefastq/environment.yml b/modules/nf-core/samtools/collatefastq/environment.yml index 04c82f1423..ec3faa9cdc 100644 --- a/modules/nf-core/samtools/collatefastq/environment.yml +++ b/modules/nf-core/samtools/collatefastq/environment.yml @@ -1,3 +1,4 @@ +name: samtools_collatefastq channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index 04c82f1423..b2150ad507 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -1,3 +1,4 @@ +name: samtools_convert channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index 04c82f1423..73badedb18 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,3 +1,4 @@ +name: samtools_faidx channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 04c82f1423..3c6f95b25a 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,3 +1,4 @@ +name: samtools_index channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index 04c82f1423..0d437d8a88 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -1,3 +1,4 @@ +name: samtools_merge channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/mpileup/environment.yml b/modules/nf-core/samtools/mpileup/environment.yml index 04c82f1423..5f06050d19 100644 --- a/modules/nf-core/samtools/mpileup/environment.yml +++ b/modules/nf-core/samtools/mpileup/environment.yml @@ -1,3 +1,4 @@ +name: samtools_mpileup channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 04c82f1423..ed4e8961af 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,3 +1,4 @@ +name: samtools_stats channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index 04c82f1423..141e7bd829 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -1,3 +1,4 @@ +name: samtools_view channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/applyvarcal/environment.yml b/modules/nf-core/sentieon/applyvarcal/environment.yml index bcd3a8b1c6..b7b5169a89 100644 --- a/modules/nf-core/sentieon/applyvarcal/environment.yml +++ b/modules/nf-core/sentieon/applyvarcal/environment.yml @@ -1,3 +1,4 @@ +name: sentieon_applyvarcal channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/bwamem/environment.yml b/modules/nf-core/sentieon/bwamem/environment.yml index bcd3a8b1c6..efd460cfa4 100644 --- a/modules/nf-core/sentieon/bwamem/environment.yml +++ b/modules/nf-core/sentieon/bwamem/environment.yml @@ -1,3 +1,4 @@ +name: sentieon_bwamem channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/dedup/environment.yml b/modules/nf-core/sentieon/dedup/environment.yml index bcd3a8b1c6..bda2b1385a 100644 --- a/modules/nf-core/sentieon/dedup/environment.yml +++ b/modules/nf-core/sentieon/dedup/environment.yml @@ -1,3 +1,4 @@ +name: sentieon_dedup channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/dnamodelapply/environment.yml b/modules/nf-core/sentieon/dnamodelapply/environment.yml index bcd3a8b1c6..3f92a79ab8 100644 --- a/modules/nf-core/sentieon/dnamodelapply/environment.yml +++ b/modules/nf-core/sentieon/dnamodelapply/environment.yml @@ -1,3 +1,4 @@ +name: sentieon_dnamodelapply channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/dnamodelapply/meta.yml b/modules/nf-core/sentieon/dnamodelapply/meta.yml index bc7d323ed5..2507654577 100644 --- a/modules/nf-core/sentieon/dnamodelapply/meta.yml +++ b/modules/nf-core/sentieon/dnamodelapply/meta.yml @@ -1,4 +1,4 @@ -name: "sentieon_dnamodelapply" +name: sentieon_dnamodelapply description: modifies the input VCF file by adding the MLrejected FILTER to the variants keywords: - dnamodelapply diff --git a/modules/nf-core/sentieon/dnascope/environment.yml b/modules/nf-core/sentieon/dnascope/environment.yml index bcd3a8b1c6..2c5b4937bf 100644 --- a/modules/nf-core/sentieon/dnascope/environment.yml +++ b/modules/nf-core/sentieon/dnascope/environment.yml @@ -1,3 +1,4 @@ +name: sentieon_dnascope channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/gvcftyper/environment.yml b/modules/nf-core/sentieon/gvcftyper/environment.yml index bcd3a8b1c6..5af2aaa8e8 100644 --- a/modules/nf-core/sentieon/gvcftyper/environment.yml +++ b/modules/nf-core/sentieon/gvcftyper/environment.yml @@ -1,3 +1,4 @@ +name: sentieon_gvcftyper channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/gvcftyper/meta.yml b/modules/nf-core/sentieon/gvcftyper/meta.yml index ceef173e3e..5a83eb0308 100644 --- a/modules/nf-core/sentieon/gvcftyper/meta.yml +++ b/modules/nf-core/sentieon/gvcftyper/meta.yml @@ -1,4 +1,4 @@ -name: SENTIEON_GVCFTYPER +name: sentieon_gvcftyper description: | Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper. keywords: diff --git a/modules/nf-core/sentieon/haplotyper/environment.yml b/modules/nf-core/sentieon/haplotyper/environment.yml index bcd3a8b1c6..5d8e4c58f9 100644 --- a/modules/nf-core/sentieon/haplotyper/environment.yml +++ b/modules/nf-core/sentieon/haplotyper/environment.yml @@ -1,3 +1,4 @@ +name: sentieon_haplotyper channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/varcal/environment.yml b/modules/nf-core/sentieon/varcal/environment.yml index bcd3a8b1c6..f04a8b78ce 100644 --- a/modules/nf-core/sentieon/varcal/environment.yml +++ b/modules/nf-core/sentieon/varcal/environment.yml @@ -1,3 +1,4 @@ +name: sentieon_varcal channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpeff/download/environment.yml b/modules/nf-core/snpeff/download/environment.yml index 7d54aa5bdb..62f3d5aad6 100644 --- a/modules/nf-core/snpeff/download/environment.yml +++ b/modules/nf-core/snpeff/download/environment.yml @@ -1,3 +1,4 @@ +name: snpeff_download channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpeff/download/meta.yml b/modules/nf-core/snpeff/download/meta.yml index 26e728f71a..f367c69664 100644 --- a/modules/nf-core/snpeff/download/meta.yml +++ b/modules/nf-core/snpeff/download/meta.yml @@ -1,4 +1,4 @@ -name: SNPEFF_DOWNLOAD +name: snpeff_download description: Genetic variant annotation and functional effect prediction toolbox keywords: - annotation diff --git a/modules/nf-core/snpeff/snpeff/environment.yml b/modules/nf-core/snpeff/snpeff/environment.yml index 7d54aa5bdb..b492e6a88e 100644 --- a/modules/nf-core/snpeff/snpeff/environment.yml +++ b/modules/nf-core/snpeff/snpeff/environment.yml @@ -1,3 +1,4 @@ +name: snpeff_snpeff channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml index 0b771447ff..7559c3de08 100644 --- a/modules/nf-core/snpeff/snpeff/meta.yml +++ b/modules/nf-core/snpeff/snpeff/meta.yml @@ -1,4 +1,4 @@ -name: SNPEFF_SNPEFF +name: snpeff_snpeff description: Genetic variant annotation and functional effect prediction toolbox keywords: - annotation diff --git a/modules/nf-core/strelka/germline/environment.yml b/modules/nf-core/strelka/germline/environment.yml index 5c9c1cf81a..23bd165b21 100644 --- a/modules/nf-core/strelka/germline/environment.yml +++ b/modules/nf-core/strelka/germline/environment.yml @@ -1,3 +1,4 @@ +name: strelka_germline channels: - conda-forge - bioconda diff --git a/modules/nf-core/strelka/somatic/environment.yml b/modules/nf-core/strelka/somatic/environment.yml index 5c9c1cf81a..ecbc865ec9 100644 --- a/modules/nf-core/strelka/somatic/environment.yml +++ b/modules/nf-core/strelka/somatic/environment.yml @@ -1,3 +1,4 @@ +name: strelka_somatic channels: - conda-forge - bioconda diff --git a/modules/nf-core/svdb/merge/environment.yml b/modules/nf-core/svdb/merge/environment.yml index e31e204e3d..4aad50da52 100644 --- a/modules/nf-core/svdb/merge/environment.yml +++ b/modules/nf-core/svdb/merge/environment.yml @@ -1,7 +1,9 @@ +name: svdb_merge channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::svdb=2.8.1 - - bioconda::samtools=1.16.1 + - svdb=2.8.1 + # renovate: datasource=conda depName=bioconda/samtools + - samtools=1.16.1 diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index fdd84057b8..028461c987 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -1,3 +1,4 @@ +name: tabix_bgziptabix channels: - conda-forge - bioconda diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index fdd84057b8..7167fb87d6 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,3 +1,4 @@ +name: tabix_tabix channels: - conda-forge - bioconda diff --git a/modules/nf-core/tiddit/sv/environment.yml b/modules/nf-core/tiddit/sv/environment.yml index 69963f7c4b..d0367f1717 100644 --- a/modules/nf-core/tiddit/sv/environment.yml +++ b/modules/nf-core/tiddit/sv/environment.yml @@ -1,3 +1,4 @@ +name: tiddit_sv channels: - conda-forge - bioconda diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 2d52ce64ac..d6917da326 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,3 +1,4 @@ +name: untar channels: - conda-forge - bioconda diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test new file mode 100644 index 0000000000..d40db13d82 --- /dev/null +++ b/modules/nf-core/untar/tests/main.nf.test @@ -0,0 +1,77 @@ +nextflow_process { + + name "Test Process UNTAR" + script "../main.nf" + process "UNTAR" + + tag "modules" + tag "modules_nfcore" + tag "untar" + + test("test_untar") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.untar).match("test_untar") }, + ) + } + + } + + test("test_untar_different_output_path") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [], file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.untar).match("test_untar_different_output_path") }, + ) + } + + } + + test("test_untar_onlyfiles") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [], file(params.test_data['generic']['tar']['tar_gz'], checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.untar).match("test_untar_onlyfiles") }, + ) + } + + } + +} diff --git 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a/modules/nf-core/vcftools/environment.yml b/modules/nf-core/vcftools/environment.yml index 875817e21d..503449e833 100644 --- a/modules/nf-core/vcftools/environment.yml +++ b/modules/nf-core/vcftools/environment.yml @@ -1,3 +1,4 @@ +name: vcftools channels: - conda-forge - bioconda diff --git a/nextflow_schema.json b/nextflow_schema.json index be354019ea..f585103b28 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -27,6 +27,7 @@ "input_restart": { "type": "string", "description": "Automatic retrieval for restart", + "fa_icon": "fas fa-file-csv", "format": "file-path", "exists": true, "mimetype": "text/csv", @@ -176,11 +177,12 @@ "type": "string", "fa_icon": "fas fa-tape", "description": "Specify UMI read structure", - "help_text": "One structure if UMI is present on one end (i.e. '+T 2M11S+T'), or two structures separated by a blank space if UMIs a present on both ends (i.e. '2M11S+T 2M11S+T'); please note, this does not handle duplex-UMIs.\n\nFor more info on UMI usage in the pipeline, also check docs [here](./docs/usage.md/#how-to-handle-umis)." + "help_text": "One structure if UMI is present on one end (i.e. '+T 2M11S+T'), or two structures separated by a blank space if UMIs a present on both ends (i.e. '2M11S+T 2M11S+T'); please note, this does not handle duplex-UMIs.\n\nFor more info on UMI usage in the pipeline, also check docs [here](./docs/usage/#how-to-handle-umis)." }, "group_by_umi_strategy": { "type": "string", "default": "Adjacency", + "fa_icon": "fas fa-tape", "description": "Default strategy with UMI", "hidden": true, "help_text": "Available values: Identity, Edit, Adjacency, Paired" diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml index 20ab756e24..f33e55023c 100644 --- a/tests/config/pytesttags.yml +++ b/tests/config/pytesttags.yml @@ -75,34 +75,34 @@ validation_checks: ## alignment_to_fastq alignment_to_fastq: - conf/modules/alignment_to_fastq.config - - modules/nf-core/cat/fastq/main.nf - - modules/nf-core/samtools/collatefastq/main.nf - - modules/nf-core/samtools/merge/main.nf - - modules/nf-core/samtools/view/main.nf - - subworkflows/local/bam_convert_samtools/main.nf + - modules/nf-core/cat/fastq/** + - modules/nf-core/samtools/collatefastq/** + - modules/nf-core/samtools/merge/** + - modules/nf-core/samtools/view/** + - subworkflows/local/bam_convert_samtools/** - tests/csv/3.0/bam_for_remapping.csv - tests/test_alignment_to_fastq.yml ## umi umi: - conf/modules/umi.config - - modules/nf-core/bwa/mem/main.nf - - modules/nf-core/bwamem2/mem/main.nf - - modules/nf-core/dragmap/align/main.nf - - modules/nf-core/fgbio/callmolecularconsensusreads/main.nf - - modules/nf-core/fgbio/fastqtobam/main.nf - - modules/nf-core/fgbio/groupreadsbyumi/main.nf - - modules/nf-core/samblaster/main.nf - - modules/nf-core/samtools/bam2fq/main.nf - - subworkflows/local/fastq_align_bwamem_mem2_dragmap/main.nf - - subworkflows/local/fastq_create_umi_consensus_fgbio/main.nf + - modules/nf-core/bwa/mem/** + - modules/nf-core/bwamem2/mem/** + - modules/nf-core/dragmap/align/** + - modules/nf-core/fgbio/callmolecularconsensusreads/** + - modules/nf-core/fgbio/fastqtobam/** + - modules/nf-core/fgbio/groupreadsbyumi/** + - modules/nf-core/samblaster/** + - modules/nf-core/samtools/bam2fq/** + - subworkflows/local/fastq_align_bwamem_mem2_dragmap/** + - subworkflows/local/fastq_create_umi_consensus_fgbio/** - tests/csv/3.0/fastq_umi.csv - tests/test_umi.yml ## fastp fastp: - conf/modules/trimming.config - - modules/nf-core/fastp/main.nf + - modules/nf-core/fastp/** - tests/csv/3.0/fastq_single.csv - tests/test_fastp.yml @@ -111,45 +111,45 @@ fastp: ### bwamem bwamem: - conf/modules/aligner.config - - modules/nf-core/bwa/mem/main.nf - - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf + - modules/nf-core/bwa/mem/** + - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/** - tests/csv/3.0/fastq_single.csv - tests/test_aligner_bwamem.yml ### bwamem2 bwamem2: - conf/modules/aligner.config - - modules/nf-core/bwamem2/mem/main.nf - - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf + - modules/nf-core/bwamem2/mem/** + - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/** - tests/csv/3.0/fastq_single.csv - tests/test_aligner_bwamem2.yml ### dragmap dragmap: - conf/modules/aligner.config - - modules/nf-core/dragmap/align/main.nf - - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf + - modules/nf-core/dragmap/align/** + - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/** - tests/csv/3.0/fastq_single.csv - tests/test_aligner_dragmap.yml ### sentieon/bwamem sentieon/bwamem: - conf/modules/aligner.config - - modules/nf-core/sentieon/bwamem/main.nf - - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf + - modules/nf-core/sentieon/bwamem/** + - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/** - tests/csv/3.0/fastq_single.csv - tests/test_sentieon_aligner_bwamem.yml ## markduplicates gatk4/markduplicates: - conf/modules/markduplicates.config - - modules/nf-core/gatk4/markduplicates/main.nf - - modules/nf-core/mosdepth/main.nf - - modules/nf-core/samtools/convert/main.nf - - modules/nf-core/samtools/index/main.nf - - modules/nf-core/samtools/stats/main.nf - - subworkflows/local/bam_markduplicates/main.nf - - subworkflows/local/cram_qc_mosdepth_samtools/main.nf + - modules/nf-core/gatk4/markduplicates/** + - modules/nf-core/mosdepth/** + - modules/nf-core/samtools/convert/** + - modules/nf-core/samtools/index/** + - modules/nf-core/samtools/stats/** + - subworkflows/local/bam_markduplicates/** + - subworkflows/local/cram_qc_mosdepth_samtools/** - tests/csv/3.0/mapped_single_bam.csv - tests/csv/3.0/mapped_single_cram.csv - tests/test_markduplicates_from_bam.yml @@ -158,12 +158,12 @@ gatk4/markduplicates: ## sentieon/dedup sentieon/dedup: - conf/modules/sentieon_dedup.config - - modules/nf-core/sentieon/bwamem/main.nf - - modules/nf-core/mosdepth/main.nf - - modules/nf-core/samtools/index/main.nf - - modules/nf-core/samtools/stats/main.nf - - subworkflows/local/bam_sentieon_dedup/main.nf - - subworkflows/local/cram_qc_mosdepth_samtools/main.nf + - modules/nf-core/sentieon/bwamem/** + - modules/nf-core/mosdepth/** + - modules/nf-core/samtools/index/** + - modules/nf-core/samtools/stats/** + - subworkflows/local/bam_sentieon_dedup/** + - subworkflows/local/cram_qc_mosdepth_samtools/** - tests/csv/3.0/mapped_single_bam.csv - tests/csv/3.0/mapped_single_cram.csv - tests/test_sentieon_dedup_from_bam.yml @@ -172,10 +172,10 @@ sentieon/dedup: ## prepare_recalibration prepare_recalibration: - conf/modules/prepare_recalibration.config - - modules/nf-core/gatk4/baserecalibrator/main.nf - - modules/nf-core/gatk4/gatherbqsrreports/main.nf - - modules/nf-core/samtools/convert/main.nf - - subworkflows/local/bam_baserecalibrator/main.nf + - modules/nf-core/gatk4/baserecalibrator/** + - modules/nf-core/gatk4/gatherbqsrreports/** + - modules/nf-core/samtools/convert/** + - subworkflows/local/bam_baserecalibrator/** - tests/csv/3.0/mapped_single_bam.csv - tests/csv/3.0/mapped_single_cram.csv - tests/test_prepare_recalibration_from_bam.yml @@ -184,12 +184,12 @@ prepare_recalibration: ## recalibrate recalibrate: - conf/modules/recalibrate.config - - modules/nf-core/gatk4/applybqsr/main.nf - - modules/nf-core/samtools/convert/main.nf - - modules/nf-core/samtools/index/main.nf - - modules/nf-core/samtools/merge/main.nf - - subworkflows/local/bam_applybqsr/main.nf - - subworkflows/local/cram_merge_index_samtools/main.nf + - modules/nf-core/gatk4/applybqsr/** + - modules/nf-core/samtools/convert/** + - modules/nf-core/samtools/index/** + - modules/nf-core/samtools/merge/** + - subworkflows/local/bam_applybqsr/** + - subworkflows/local/cram_merge_index_samtools/** - tests/csv/3.0/prepare_recalibration_single_bam.csv - tests/csv/3.0/prepare_recalibration_single_cram.csv - tests/test_recalibrate_from_bam.yml @@ -198,11 +198,11 @@ recalibrate: ## intervals intervals: - conf/modules/prepare_intervals.config - - modules/local/build_intervals/main.nf - - modules/local/create_intervals_bed/main.nf - - modules/nf-core/gatk4/intervallisttobed/main.nf - - modules/nf-core/tabix/bgziptabix/main.nf - - subworkflows/local/prepare_intervals/main.nf + - modules/local/build_intervals/** + - modules/local/create_intervals_bed/** + - modules/nf-core/gatk4/intervallisttobed/** + - modules/nf-core/tabix/bgziptabix/** + - subworkflows/local/prepare_intervals/** - tests/csv/3.0/fastq_single.csv - tests/test_intervals.yml @@ -211,13 +211,13 @@ gatk4spark: - conf/modules/markduplicates.config - conf/modules/prepare_recalibration.config - conf/modules/recalibrate.config - - modules/nf-core/gatk4spark/applybqsr/main.nf - - modules/nf-core/gatk4spark/baserecalibrator/main.nf - - modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf - - modules/nf-core/gatk4spark/markduplicates/main.nf - - subworkflows/local/bam_applybqsr_spark/main.nf - - subworkflows/local/bam_baserecalibrator_spark/main.nf - - subworkflows/local/bam_markduplicates_spark/main.nf + - modules/nf-core/gatk4spark/applybqsr/** + - modules/nf-core/gatk4spark/baserecalibrator/** + - modules/nf-core/gatk4/estimatelibrarycomplexity/** + - modules/nf-core/gatk4spark/markduplicates/** + - subworkflows/local/bam_applybqsr_spark/** + - subworkflows/local/bam_baserecalibrator_spark/** + - subworkflows/local/bam_markduplicates_spark/** - tests/csv/3.0/fastq_single.csv - tests/test_gatk4spark.yml @@ -226,14 +226,14 @@ gatk4spark: ## cnvkit cnvkit: - conf/modules/cnvkit.config - - modules/nf-core/cnvkit/antitarget/main.nf - - modules/nf-core/cnvkit/batch/main.nf - - modules/nf-core/cnvkit/reference/main.nf - - subworkflows/local/bam_variant_calling_cnvkit/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_somatic_all/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - - subworkflows/local/prepare_reference_cnvkit/main.nf + - modules/nf-core/cnvkit/antitarget/** + - modules/nf-core/cnvkit/batch/** + - modules/nf-core/cnvkit/reference/** + - subworkflows/local/bam_variant_calling_cnvkit/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_somatic_all/** + - subworkflows/local/bam_variant_calling_tumor_only_all/** + - subworkflows/local/prepare_reference_cnvkit/** - tests/csv/3.0/recalibrated_germline.csv - tests/csv/3.0/recalibrated_somatic.csv - tests/csv/3.0/recalibrated_tumoronly.csv @@ -243,18 +243,18 @@ cnvkit: controlfreec: - conf/modules/controlfreec.config - conf/modules/mpileup.config - - modules/nf-core/cat/cat/main.nf - - modules/nf-core/controlfreec/assesssignificance/main.nf - - modules/nf-core/controlfreec/freec/main.nf - - modules/nf-core/controlfreec/freec2bed/main.nf - - modules/nf-core/controlfreec/freec2circos/main.nf - - modules/nf-core/controlfreec/makegraph/main.nf - - modules/nf-core/samtools/mpileup/main.nf - - subworkflows/local/bam_variant_calling_mpileup/main.nf - - subworkflows/local/bam_variant_calling_somatic_all/main.nf - - subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf + - modules/nf-core/cat/cat/** + - modules/nf-core/controlfreec/assesssignificance/** + - modules/nf-core/controlfreec/freec/** + - modules/nf-core/controlfreec/freec2bed/** + - modules/nf-core/controlfreec/freec2circos/** + - modules/nf-core/controlfreec/makegraph/** + - modules/nf-core/samtools/mpileup/** + - subworkflows/local/bam_variant_calling_mpileup/** + - subworkflows/local/bam_variant_calling_somatic_all/** + - subworkflows/local/bam_variant_calling_somatic_controlfreec/** + - subworkflows/local/bam_variant_calling_tumor_only_all/** + - subworkflows/local/bam_variant_calling_tumor_only_controlfreec/** - tests/csv/3.0/recalibrated_somatic.csv - tests/csv/3.0/recalibrated_tumoronly.csv - tests/test_controlfreec.yml @@ -262,25 +262,25 @@ controlfreec: ## deepvariant deepvariant: - conf/modules/deepvariant.config - - modules/nf-core/deepvariant/main.nf - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/tabix/tabix/main.nf - - subworkflows/local/bam_variant_calling_deepvariant/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf + - modules/nf-core/deepvariant/** + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/tabix/tabix/** + - subworkflows/local/bam_variant_calling_deepvariant/** + - subworkflows/local/bam_variant_calling_germline_all/** - tests/csv/3.0/recalibrated_germline.csv - tests/test_deepvariant.yml ## freebayes freebayes: - conf/modules/freebayes.config - - modules/nf-core/bcftools/sort/main.nf - - modules/nf-core/freebayes/main.nf - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/tabix/tabix/main.nf - - subworkflows/local/bam_variant_calling_freebayes/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_somatic_all/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf + - modules/nf-core/bcftools/sort/** + - modules/nf-core/freebayes/** + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/tabix/tabix/** + - subworkflows/local/bam_variant_calling_freebayes/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_somatic_all/** + - subworkflows/local/bam_variant_calling_tumor_only_all/** - tests/csv/3.0/fastq_pair.csv - tests/csv/3.0/fastq_single.csv - tests/csv/3.0/recalibrated_tumoronly.csv @@ -289,103 +289,103 @@ freebayes: ## haplotypecaller haplotypecaller: - conf/modules/haplotypecaller.config - - modules/nf-core/gatk4/cnnscorevariants/main.nf - - modules/nf-core/gatk4/filtervarianttranches/main.nf - - modules/nf-core/gatk4/haplotypecaller/main.nf - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/samtools/index/main.nf - - modules/nf-core/samtools/merge/main.nf - - subworkflows/local/bam_merge_index_samtools/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf - - subworkflows/local/vcf_variant_filtering_gatk/main.nf + - modules/nf-core/gatk4/cnnscorevariants/** + - modules/nf-core/gatk4/filtervarianttranches/** + - modules/nf-core/gatk4/haplotypecaller/** + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/samtools/index/** + - modules/nf-core/samtools/merge/** + - subworkflows/local/bam_merge_index_samtools/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_haplotypecaller/** + - subworkflows/local/vcf_variant_filtering_gatk/** - tests/csv/3.0/mapped_single_bam.csv - tests/test_haplotypecaller.yml haplotypecaller_skip_filter: - conf/modules/haplotypecaller.config - - modules/nf-core/gatk4/haplotypecaller/main.nf - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/samtools/index/main.nf - - modules/nf-core/samtools/merge/main.nf - - subworkflows/local/bam_merge_index_samtools/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf + - modules/nf-core/gatk4/haplotypecaller/** + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/samtools/index/** + - modules/nf-core/samtools/merge/** + - subworkflows/local/bam_merge_index_samtools/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_haplotypecaller/** - tests/csv/3.0/mapped_single_bam.csv - tests/test_haplotypecaller_skip_filter.yml ## sentieon/dnascope sentieon/dnascope: - conf/modules/sentieon_dnascope.config - - modules/nf-core/sentieon/dnascope/main.nf - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/samtools/index/main.nf - - modules/nf-core/samtools/merge/main.nf - - subworkflows/local/bam_merge_index_samtools/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf + - modules/nf-core/sentieon/dnascope/** + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/samtools/index/** + - modules/nf-core/samtools/merge/** + - subworkflows/local/bam_merge_index_samtools/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_sentieon_dnascope/** - tests/csv/3.0/mapped_single_bam.csv - tests/test_sentieon_dnascope.yml sentieon_dnascope_skip_filter: - conf/modules/sentieon_dnascope.config - - modules/nf-core/sentieon/dnascope/main.nf - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/samtools/index/main.nf - - modules/nf-core/samtools/merge/main.nf - - subworkflows/local/bam_merge_index_samtools/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf + - modules/nf-core/sentieon/dnascope/** + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/samtools/index/** + - modules/nf-core/samtools/merge/** + - subworkflows/local/bam_merge_index_samtools/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_sentieon_dnascope/** - tests/csv/3.0/mapped_single_bam.csv - tests/test_sentieon_dnascope_skip_filter.yml ## sentieon/haplotyper sentieon/haplotyper: - conf/modules/sentieon_haplotyper.config - - modules/nf-core/gatk4/cnnscorevariants/main.nf - - modules/nf-core/gatk4/filtervarianttranches/main.nf - - modules/nf-core/sentieon/haplotyper/main.nf - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/samtools/index/main.nf - - modules/nf-core/samtools/merge/main.nf - - subworkflows/local/bam_merge_index_samtools/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf - - subworkflows/local/vcf_variant_filtering_gatk/main.nf + - modules/nf-core/gatk4/cnnscorevariants/** + - modules/nf-core/gatk4/filtervarianttranches/** + - modules/nf-core/sentieon/haplotyper/** + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/samtools/index/** + - modules/nf-core/samtools/merge/** + - subworkflows/local/bam_merge_index_samtools/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_sentieon_haplotyper/** + - subworkflows/local/vcf_variant_filtering_gatk/** - tests/csv/3.0/mapped_single_bam.csv - tests/test_sentieon_haplotyper.yml sentieon_haplotyper_skip_filter: - conf/modules/sentieon_haplotyper.config - - modules/nf-core/sentieon/haplotyper/main.nf - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/samtools/index/main.nf - - modules/nf-core/samtools/merge/main.nf - - subworkflows/local/bam_merge_index_samtools/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf + - modules/nf-core/sentieon/haplotyper/** + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/samtools/index/** + - modules/nf-core/samtools/merge/** + - subworkflows/local/bam_merge_index_samtools/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_sentieon_haplotyper/** - tests/csv/3.0/mapped_single_bam.csv - tests/test_sentieon_haplotyper_skip_filter.yml ## joint_germline joint_germline: - conf/modules/haplotypecaller.config - - modules/nf-core/bcftools/sort/main.nf - - modules/nf-core/gatk4/applyvqsr/main.nf - - modules/nf-core/gatk4/cnnscorevariants/main.nf - - modules/nf-core/gatk4/filtervarianttranches/main.nf - - modules/nf-core/gatk4/genomicsdbimport/main.nf - - modules/nf-core/gatk4/genotypegvcfs/main.nf - - modules/nf-core/gatk4/haplotypecaller/main.nf - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/gatk4/variantrecalibrator/main.nf - - modules/nf-core/samtools/index/main.nf - - modules/nf-core/samtools/merge/main.nf - - subworkflows/local/bam_joint_calling_germline_gatk/main.nf - - subworkflows/local/bam_merge_index_samtools/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf - - subworkflows/local/vcf_variant_filtering_gatk/main.nf + - modules/nf-core/bcftools/sort/** + - modules/nf-core/gatk4/applyvqsr/** + - modules/nf-core/gatk4/cnnscorevariants/** + - modules/nf-core/gatk4/filtervarianttranches/** + - modules/nf-core/gatk4/genomicsdbimport/** + - modules/nf-core/gatk4/genotypegvcfs/** + - modules/nf-core/gatk4/haplotypecaller/** + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/gatk4/variantrecalibrator/** + - modules/nf-core/samtools/index/** + - modules/nf-core/samtools/merge/** + - subworkflows/local/bam_joint_calling_germline_gatk/** + - subworkflows/local/bam_merge_index_samtools/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_haplotypecaller/** + - subworkflows/local/vcf_variant_filtering_gatk/** - tests/csv/3.0/mapped_joint_bam.csv - tests/test_joint_germline.yml @@ -394,9 +394,9 @@ sentieon_dnascope_joint_germline: - conf/modules/prepare_genome.config - conf/modules/sentieon_dnascope.config - conf/modules/sentieon_dnascope_joint_germline.config - - modules/nf-core/sentieon/dnascope/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf + - modules/nf-core/sentieon/dnascope/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_sentieon_dnascope/** - tests/csv/3.0/mapped_joint_bam.csv - tests/test_sentieon_dnascop_joint_germline.yml @@ -405,25 +405,25 @@ sentieon_haplotyper_joint_germline: - conf/modules/prepare_genome.config - conf/modules/sentieon_haplotyper.config - conf/modules/sentieon_haplotyper_joint_germline.config - - modules/nf-core/sentieon/haplotyper/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf + - modules/nf-core/sentieon/haplotyper/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_sentieon_haplotyper/** - tests/csv/3.0/mapped_joint_bam.csv - tests/test_sentieon_haplotyper_joint_germline.yml ## manta manta: - conf/modules/manta.config - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/manta/germline/main.nf - - modules/nf-core/manta/somatic/main.nf - - modules/nf-core/manta/tumoronly/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_germline_manta/main.nf - - subworkflows/local/bam_variant_calling_somatic_all/main.nf - - subworkflows/local/bam_variant_calling_somatic_manta/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/manta/germline/** + - modules/nf-core/manta/somatic/** + - modules/nf-core/manta/tumoronly/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_germline_manta/** + - subworkflows/local/bam_variant_calling_somatic_all/** + - subworkflows/local/bam_variant_calling_somatic_manta/** + - subworkflows/local/bam_variant_calling_tumor_only_all/** + - subworkflows/local/bam_variant_calling_tumor_only_manta/** - tests/csv/3.0/recalibrated_germline.csv - tests/csv/3.0/recalibrated_somatic.csv - tests/csv/3.0/recalibrated_tumoronly.csv @@ -432,12 +432,12 @@ manta: ## mpileup mpileup: - conf/modules/mpileup.config - - modules/nf-core/cat/cat/main.nf - - modules/nf-core/samtools/mpileup/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_mpileup/main.nf - - subworkflows/local/bam_variant_calling_somatic_all/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf + - modules/nf-core/cat/cat/** + - modules/nf-core/samtools/mpileup/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_mpileup/** + - subworkflows/local/bam_variant_calling_somatic_all/** + - subworkflows/local/bam_variant_calling_tumor_only_all/** - tests/csv/3.0/recalibrated_germline.csv - tests/csv/3.0/recalibrated_tumoronly.csv - tests/test_mpileup.yml @@ -445,41 +445,41 @@ mpileup: ## msisensorpro msisensorpro: - conf/modules/msisensorpro.config - - modules/nf-core/msisensorpro/msi_somatic/main.nf - - modules/nf-core/msisensorpro/scan/main.nf - - subworkflows/local/bam_variant_calling_somatic_all/main.nf + - modules/nf-core/msisensorpro/msi_somatic/** + - modules/nf-core/msisensorpro/scan/** + - subworkflows/local/bam_variant_calling_somatic_all/** - tests/csv/3.0/recalibrated_somatic.csv - tests/test_msisensorpro.yml ## mutect2 mutect2: - conf/modules/mutect2.config - - modules/nf-core/gatk4/calculatecontamination/main.nf - - modules/nf-core/gatk4/filtermutectcalls/main.nf - - modules/nf-core/gatk4/gatherpileupsummaries/main.nf - - modules/nf-core/gatk4/getpileupsummaries/main.nf - - modules/nf-core/gatk4/learnreadorientationmodel/main.nf - - modules/nf-core/gatk4/mergemutectstats/main.nf - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/gatk4/mutect2/main.nf - - subworkflows/local/bam_variant_calling_somatic_all/main.nf - - subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf + - modules/nf-core/gatk4/calculatecontamination/** + - modules/nf-core/gatk4/filtermutectcalls/** + - modules/nf-core/gatk4/gatherpileupsummaries/** + - modules/nf-core/gatk4/getpileupsummaries/** + - modules/nf-core/gatk4/learnreadorientationmodel/** + - modules/nf-core/gatk4/mergemutectstats/** + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/gatk4/mutect2/** + - subworkflows/local/bam_variant_calling_somatic_all/** + - subworkflows/local/bam_variant_calling_somatic_mutect2/** + - subworkflows/local/bam_variant_calling_tumor_only_all/** + - subworkflows/local/bam_variant_calling_tumor_only_mutect2/** - tests/csv/3.0/recalibrated_tumoronly.csv - tests/test_mutect2.yml ## strelka strelka: - conf/modules/strelka.config - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/strelka/germline/main.nf - - modules/nf-core/strelka/somatic/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_single_strelka/main.nf - - subworkflows/local/bam_variant_calling_somatic_all/main.nf - - subworkflows/local/bam_variant_calling_somatic_strelka/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/strelka/germline/** + - modules/nf-core/strelka/somatic/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_single_strelka/** + - subworkflows/local/bam_variant_calling_somatic_all/** + - subworkflows/local/bam_variant_calling_somatic_strelka/** + - subworkflows/local/bam_variant_calling_tumor_only_all/** - tests/csv/3.0/recalibrated_germline.csv - tests/csv/3.0/recalibrated_somatic.csv - tests/csv/3.0/recalibrated_tumoronly.csv @@ -490,28 +490,28 @@ strelka: strelka_bp: - conf/modules/manta.config - conf/modules/strelka.config - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/manta/somatic/main.nf - - modules/nf-core/strelka/somatic/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_somatic_all/main.nf - - subworkflows/local/bam_variant_calling_somatic_manta/main.nf - - subworkflows/local/bam_variant_calling_somatic_strelka/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/manta/somatic/** + - modules/nf-core/strelka/somatic/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_somatic_all/** + - subworkflows/local/bam_variant_calling_somatic_manta/** + - subworkflows/local/bam_variant_calling_somatic_strelka/** + - subworkflows/local/bam_variant_calling_tumor_only_all/** - tests/csv/3.0/recalibrated_somatic.csv - tests/test_strelka_bp.yml ## tiddit tiddit: - conf/modules/tiddit.config - - modules/nf-core/svdb/merge/main.nf.nf - - modules/nf-core/tabix/bgziptabix/main.nf - - modules/nf-core/tiddit/sv/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_single_tiddit/main.nf - - subworkflows/local/bam_variant_calling_somatic_all/main.nf - - subworkflows/local/bam_variant_calling_somatic_tiddit/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf + - modules/nf-core/svdb/merge/**.nf + - modules/nf-core/tabix/bgziptabix/** + - modules/nf-core/tiddit/sv/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_single_tiddit/** + - subworkflows/local/bam_variant_calling_somatic_all/** + - subworkflows/local/bam_variant_calling_somatic_tiddit/** + - subworkflows/local/bam_variant_calling_tumor_only_all/** - tests/csv/3.0/recalibrated_germline.csv - tests/csv/3.0/recalibrated_somatic.csv - tests/csv/3.0/recalibrated_tumoronly.csv @@ -522,47 +522,47 @@ tiddit: ## cache cache: - conf/modules/prepare_cache.config - - modules/nf-core/ensemblvep/download/main.nf - - modules/nf-core/snpeff/download/main.nf - - subworkflows/local/prepare_cache/main.nf + - modules/nf-core/ensemblvep/download/** + - modules/nf-core/snpeff/download/** + - subworkflows/local/prepare_cache/** - tests/test_annotation_cache.yml ## merge merge: - conf/modules/annotate.config - - modules/nf-core/ensemblvep/vep/main.nf - - modules/nf-core/snpeff/snpeff/main.nf - - modules/nf-core/tabix/bgziptabix/main.nf - - subworkflows/local/vcf_annotate_all/main.nf - - subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf - - subworkflows/nf-core/vcf_annotate_snpeff/main.nf + - modules/nf-core/ensemblvep/vep/** + - modules/nf-core/snpeff/snpeff/** + - modules/nf-core/tabix/bgziptabix/** + - subworkflows/local/vcf_annotate_all/** + - subworkflows/nf-core/vcf_annotate_ensemblvep/** + - subworkflows/nf-core/vcf_annotate_snpeff/** - tests/csv/3.0/vcf_single.csv - tests/test_annotation_merge.yml ## snpeff snpeff: - conf/modules/annotate.config - - modules/nf-core/snpeff/snpeff/main.nf - - modules/nf-core/tabix/bgziptabix/main.nf - - subworkflows/nf-core/vcf_annotate_snpeff/main.nf + - modules/nf-core/snpeff/snpeff/** + - modules/nf-core/tabix/bgziptabix/** + - subworkflows/nf-core/vcf_annotate_snpeff/** - tests/csv/3.0/vcf_single.csv - tests/test_annotation_snpeff.yml ## vep vep: - conf/modules/annotate.config - - modules/nf-core/ensemblvep/vep/main.nf - - modules/nf-core/tabix/bgziptabix/main.nf - - subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf + - modules/nf-core/ensemblvep/vep/** + - modules/nf-core/tabix/bgziptabix/** + - subworkflows/nf-core/vcf_annotate_ensemblvep/** - tests/csv/3.0/vcf_single.csv - tests/test_annotation_vep.yml ## bcfann bcfann: - conf/modules/annotate.config - - modules/nf-core/bcftools/annotate/main.nf - - modules/nf-core/tabix/bgziptabix/main.nf - - subworkflows/nf-core/vcf_annotate_bcftools/main.nf + - modules/nf-core/bcftools/annotate/** + - modules/nf-core/tabix/bgziptabix/** + - subworkflows/nf-core/vcf_annotate_bcftools/** - tests/csv/3.0/vcf_single.csv - tests/test_annotation_bcfann.yml @@ -571,31 +571,31 @@ bcfann: ## concatenate germline vcfs concatenate_vcfs: - conf/modules/post_variant_calling.config - - modules/nf-core/bcftools/concat/main.nf - - modules/nf-core/bcftools/mpileup/main.nf - - modules/nf-core/bcftools/sort/main.nf - - modules/nf-core/deepvariant/main.nf - - modules/nf-core/freebayes/main.nf - - modules/nf-core/gatk4/haplotypecaller/main.nf - - modules/nf-core/gatk4/mergevcfs/main.nf - - modules/nf-core/manta/germline/main.nf - - modules/nf-core/samtools/mpileup/main.nf - - modules/nf-core/strelka/germline/main.nf - - modules/nf-core/tabix/bgziptabix/main.nf - - modules/nf-core/tabix/tabix/main.nf - - modules/nf-core/tiddit/sv/main.nf - - subworkflows/local/bam_variant_calling_deepvariant/main.nf - - subworkflows/local/bam_variant_calling_freebayes/main.nf - - subworkflows/local/bam_variant_calling_germline_all/main.nf - - subworkflows/local/bam_variant_calling_germline_manta/main.nf - - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf - - subworkflows/local/bam_variant_calling_mpileup/main.nf - - subworkflows/local/bam_variant_calling_single_strelka/main.nf - - subworkflows/local/bam_variant_calling_single_tiddit/main.nf - - subworkflows/local/bam_variant_calling_somatic_all/main.nf - - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - - subworkflows/local/post_variantcalling/main.nf - - subworkflows/local/vcf_concatenate_germline/main.nf + - modules/nf-core/bcftools/concat/** + - modules/nf-core/bcftools/mpileup/** + - modules/nf-core/bcftools/sort/** + - modules/nf-core/deepvariant/** + - modules/nf-core/freebayes/** + - modules/nf-core/gatk4/haplotypecaller/** + - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/manta/germline/** + - modules/nf-core/samtools/mpileup/** + - modules/nf-core/strelka/germline/** + - modules/nf-core/tabix/bgziptabix/** + - modules/nf-core/tabix/tabix/** + - modules/nf-core/tiddit/sv/** + - subworkflows/local/bam_variant_calling_deepvariant/** + - subworkflows/local/bam_variant_calling_freebayes/** + - subworkflows/local/bam_variant_calling_germline_all/** + - subworkflows/local/bam_variant_calling_germline_manta/** + - subworkflows/local/bam_variant_calling_haplotypecaller/** + - subworkflows/local/bam_variant_calling_mpileup/** + - subworkflows/local/bam_variant_calling_single_strelka/** + - subworkflows/local/bam_variant_calling_single_tiddit/** + - subworkflows/local/bam_variant_calling_somatic_all/** + - subworkflows/local/bam_variant_calling_tumor_only_all/** + - subworkflows/local/post_variantcalling/** + - subworkflows/local/vcf_concatenate_germline/** - tests/csv/3.0/mapped_joint_bam.csv - tests/test_concat_germline_vcfs.yml @@ -604,8 +604,8 @@ concatenate_vcfs: ## ngscheckmate ngscheckmate: - conf/modules/ngscheckmate.config - - modules/nf-core/bcftools/mpileup/main.nf - - modules/nf-core/ngscheckmate/ncm/main.nf - - subworkflows/local/cram_sampleqc/main.nf + - modules/nf-core/bcftools/mpileup/** + - modules/nf-core/ngscheckmate/ncm/** + - subworkflows/local/cram_sampleqc/** - subworkflows/nf-core/bam_ngscheckmate/** - tests/test_ngscheckmate.yml