diff --git a/modules/leehom/meta.yml b/modules/leehom/meta.yml index 658db227..05a52743 100644 --- a/modules/leehom/meta.yml +++ b/modules/leehom/meta.yml @@ -61,11 +61,11 @@ output: pattern: "*.r1.fail.fq.gz" - unmerged_r2_fq_pass: type: file - description: Passed unmerged R1 FASTQs + description: Passed unmerged R2 FASTQs pattern: "*.r2.fq.gz" - unmerged_r2_fq_pass: type: file - description: Failed unmerged R1 FASTQs + description: Failed unmerged R2 FASTQs pattern: "*.r2.fail.fq.gz" - log: type: file diff --git a/modules/picard/cleansam/main.nf b/modules/picard/cleansam/main.nf index 2eb171d5..fb435911 100644 --- a/modules/picard/cleansam/main.nf +++ b/modules/picard/cleansam/main.nf @@ -1,6 +1,6 @@ process PICARD_CLEANSAM { tag "$meta.id" - label 'process_low' + label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.26.9" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -8,10 +8,10 @@ process PICARD_CLEANSAM { 'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }" input: - tuple val(meta), path(sam) + tuple val(meta), path(bam) output: - tuple val(meta), path("*.sam"), emit: sam + tuple val(meta), path("*.bam"), emit: bam path "versions.yml" , emit: versions when: @@ -20,7 +20,6 @@ process PICARD_CLEANSAM { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def STRINGENCY = task.ext.stringency ?: "STRICT" def avail_mem = 3 if (!task.memory) { log.info '[Picard CleanSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' @@ -32,9 +31,8 @@ process PICARD_CLEANSAM { -Xmx${avail_mem}g \\ CleanSam \\ ${args} \\ - -I ${sam} \\ - -O ${prefix}.sam \\ - --VALIDATION_STRINGENCY ${STRINGENCY} + -I ${bam} \\ + -O ${prefix}.bam cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/picard/cleansam/meta.yml b/modules/picard/cleansam/meta.yml index d22e1742..11d8b7c4 100644 --- a/modules/picard/cleansam/meta.yml +++ b/modules/picard/cleansam/meta.yml @@ -1,8 +1,7 @@ name: picard_cleansam -description: Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads +description: Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads keywords: - clean - - sam - bam tools: - picard: @@ -22,8 +21,8 @@ input: e.g. [ id:'test', single_end:false ] - sam: type: file - description: SAM file - pattern: "*.{sam}" + description: BAM file + pattern: "*.{bam}" output: - meta: @@ -37,8 +36,8 @@ output: pattern: "versions.yml" - sam: type: file - description: Cleaned SAM file - pattern: "*.{sam}" + description: Cleaned BAM file + pattern: "*.{bam}" authors: - "@sateeshperi" diff --git a/tests/modules/picard/cleansam/test.yml b/tests/modules/picard/cleansam/test.yml index 716dfe6a..3b235d07 100644 --- a/tests/modules/picard/cleansam/test.yml +++ b/tests/modules/picard/cleansam/test.yml @@ -4,7 +4,7 @@ - picard/cleansam - picard files: - - path: output/picard/test.sam - md5sum: e314171a6060eb79947c13ad126ddf00 + - path: output/picard/test.bam + md5sum: a48f8e77a1480445efc57570c3a38a68 - path: output/picard/versions.yml md5sum: e6457d7c6de51bf6f4b577eda65e57ac