From 6223c35a9cbe37f5f4e90a7d465d5c955a84b19f Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 30 Aug 2023 06:57:33 +0000 Subject: [PATCH] Modules updates --- modules.json | 16 ++++++++-------- modules/local/mirtop_quant.nf | 4 ++-- modules/local/samplesheet_check.nf | 1 - .../nf-core/custom/dumpsoftwareversions/main.nf | 6 +++--- modules/nf-core/fastp/main.nf | 6 +++--- modules/nf-core/fastqc/main.nf | 6 +++++- modules/nf-core/multiqc/main.nf | 6 +++--- modules/nf-core/samtools/flagstat/main.nf | 11 +++++++++++ modules/nf-core/samtools/idxstats/main.nf | 12 ++++++++++++ modules/nf-core/samtools/sort/main.nf | 2 -- modules/nf-core/samtools/stats/main.nf | 2 +- modules/nf-core/samtools/stats/meta.yml | 10 ++++++++-- 12 files changed, 56 insertions(+), 26 deletions(-) diff --git a/modules.json b/modules.json index 0b6daac5..defa77af 100644 --- a/modules.json +++ b/modules.json @@ -12,32 +12,32 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", "installed_by": ["modules"] }, "fastp": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c", "installed_by": ["modules"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639", "installed_by": ["modules"] }, "samtools/index": { @@ -47,12 +47,12 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9", "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", "installed_by": ["modules"] } } diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf index 3ebb65ac..cc8d29a7 100644 --- a/modules/local/mirtop_quant.nf +++ b/modules/local/mirtop_quant.nf @@ -12,9 +12,9 @@ process MIRTOP_QUANT { path gtf output: - path "mirtop/mirtop.gff" + path "mirtop/mirtop.gff" , emit: mirtop_gff path "mirtop/mirtop.tsv" , emit: mirtop_table - path "mirtop/mirtop_rawData.tsv" + path "mirtop/mirtop_rawData.tsv", emit: mirtop_rawdata path "mirtop/stats/*" , emit: logs path "versions.yml" , emit: versions diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index c1b0967f..351d2322 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -1,5 +1,4 @@ process SAMPLESHEET_CHECK { - label 'process_low' tag "$samplesheet" label 'process_single' diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..c9d014b1 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 2ca2d3ee..831b7f12 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -2,10 +2,10 @@ process FASTP { tag "$meta.id" label 'process_medium' - conda "bioconda::fastp=0.23.2" + conda "bioconda::fastp=0.23.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' : - 'biocontainers/fastp:0.23.2--h79da9fb_0' }" + 'https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0' : + 'biocontainers/fastp:0.23.4--h5f740d0_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 07d5e433..249f9064 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -29,7 +29,11 @@ process FASTQC { printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name done - fastqc $args --threads $task.cpus $renamed_files + + fastqc \\ + $args \\ + --threads $task.cpus \\ + $renamed_files cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1fc387be..65d7dd0d 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index eb7e72fc..b75707ec 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -32,4 +32,15 @@ process SAMTOOLS_FLAGSTAT { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.flagstat + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index a257d700..83c7c34b 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -33,4 +33,16 @@ process SAMTOOLS_IDXSTATS { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.idxstats + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 1e5181d4..2b7753fd 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -21,13 +21,11 @@ process SAMTOOLS_SORT { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def sort_memory = (task.memory.mega/task.cpus).intValue() if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ samtools sort \\ $args \\ -@ $task.cpus \\ - -m ${sort_memory}M \\ -o ${prefix}.bam \\ -T $prefix \\ $bam diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index eb7f098b..4a2607de 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -9,7 +9,7 @@ process SAMTOOLS_STATS { input: tuple val(meta), path(input), path(input_index) - path fasta + tuple val(meta2), path(fasta) output: tuple val(meta), path("*.stats"), emit: stats diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 1d68a5d8..90e6345f 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -30,9 +30,14 @@ input: type: file description: BAI/CRAI file from alignment pattern: "*.{bai,crai}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fasta: - type: optional file - description: Reference file the CRAM was created with + type: file + description: Reference file the CRAM was created with (optional) pattern: "*.{fasta,fa}" output: - meta: @@ -51,3 +56,4 @@ output: authors: - "@drpatelh" - "@FriederikeHanssen" + - "@ramprasadn"