Merge branch 'dev' into fix_fulltest

FriederikeHanssen · Nov 15, 2023 · c46c354 · c46c354
2 parents 0d36a50 + 4f0cc6d
commit c46c354
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diff --git 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
@@ -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
@@ -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
@@ -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
diff --git 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
@@ -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
@@ -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
diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml
diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml
diff --git a/modules/nf-core/bcftools/mpileup/environment.yml b/modules/nf-core/bcftools/mpileup/environment.yml
diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml
diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml
diff --git a/modules/nf-core/bwa/index/environment.yml b/modules/nf-core/bwa/index/environment.yml
diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml
diff --git a/modules/nf-core/bwamem2/index/environment.yml b/modules/nf-core/bwamem2/index/environment.yml
diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml
diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml
diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
diff --git a/modules/nf-core/cnvkit/antitarget/environment.yml b/modules/nf-core/cnvkit/antitarget/environment.yml
diff --git a/modules/nf-core/cnvkit/batch/environment.yml b/modules/nf-core/cnvkit/batch/environment.yml
diff --git a/modules/nf-core/cnvkit/genemetrics/environment.yml b/modules/nf-core/cnvkit/genemetrics/environment.yml
diff --git a/modules/nf-core/cnvkit/reference/environment.yml b/modules/nf-core/cnvkit/reference/environment.yml
diff --git a/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff b/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff
diff --git a/modules/nf-core/controlfreec/assesssignificance/environment.yml b/modules/nf-core/controlfreec/assesssignificance/environment.yml
diff --git a/modules/nf-core/controlfreec/freec/environment.yml b/modules/nf-core/controlfreec/freec/environment.yml
diff --git a/modules/nf-core/controlfreec/freec2bed/environment.yml b/modules/nf-core/controlfreec/freec2bed/environment.yml
diff --git a/modules/nf-core/controlfreec/freec2circos/environment.yml b/modules/nf-core/controlfreec/freec2circos/environment.yml
diff --git a/modules/nf-core/controlfreec/makegraph/environment.yml b/modules/nf-core/controlfreec/makegraph/environment.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/modules/nf-core/deepvariant/environment.yml b/modules/nf-core/deepvariant/environment.yml
diff --git a/modules/nf-core/dragmap/align/environment.yml b/modules/nf-core/dragmap/align/environment.yml
diff --git a/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff b/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff
diff --git a/modules/nf-core/dragmap/hashtable/environment.yml b/modules/nf-core/dragmap/hashtable/environment.yml
diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml
diff --git a/modules/nf-core/ensemblvep/download/meta.yml b/modules/nf-core/ensemblvep/download/meta.yml
diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml
diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml
diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml b/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml
diff --git a/modules/nf-core/fgbio/fastqtobam/environment.yml b/modules/nf-core/fgbio/fastqtobam/environment.yml
diff --git a/modules/nf-core/fgbio/groupreadsbyumi/environment.yml b/modules/nf-core/fgbio/groupreadsbyumi/environment.yml
diff --git a/modules/nf-core/freebayes/environment.yml b/modules/nf-core/freebayes/environment.yml
diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml
diff --git a/modules/nf-core/gatk4/applyvqsr/environment.yml b/modules/nf-core/gatk4/applyvqsr/environment.yml
diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml
diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml
diff --git a/modules/nf-core/gatk4/cnnscorevariants/environment.yml b/modules/nf-core/gatk4/cnnscorevariants/environment.yml
diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml
diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml
diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml
diff --git a/modules/nf-core/gatk4/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml
diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml
diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml
diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml
diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml
diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml