diff --git a/modules.json b/modules.json index f7da822..81077ac 100644 --- a/modules.json +++ b/modules.json @@ -74,8 +74,7 @@ "samtools/view": { "branch": "master", "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f", - "installed_by": ["modules"], - "patch": "modules/nf-core/samtools/view/samtools-view.diff" + "installed_by": ["modules"] }, "untar": { "branch": "master", diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index aea5a42..cb91fac 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -13,14 +13,13 @@ process SAMTOOLS_VIEW { path qname output: - tuple val(meta), path("*.bam"), emit: bam, optional: true - tuple val(meta), path("*.cram"), emit: cram, optional: true - tuple val(meta), path("*.sam"), emit: sam, optional: true - tuple val(meta), path("*.bai"), emit: bai, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - tuple val(meta), path("*.unoutput"), emit: unoutput, optional: true - path "versions.yml", emit: versions + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.sam"), emit: sam, optional: true + tuple val(meta), path("*.bai"), emit: bai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -30,7 +29,7 @@ process SAMTOOLS_VIEW { def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--reference ${fasta}" : "" - def readnames = qname ? "--qname-file ${qname} --unoutput ${prefix}.unoutput": "" + def readnames = qname ? "--qname-file ${qname}": "" def file_type = args.contains("--output-fmt sam") ? "sam" : args.contains("--output-fmt bam") ? "bam" : args.contains("--output-fmt cram") ? "cram" : diff --git a/modules/nf-core/samtools/view/samtools-view.diff b/modules/nf-core/samtools/view/samtools-view.diff deleted file mode 100644 index 49c9241..0000000 --- a/modules/nf-core/samtools/view/samtools-view.diff +++ /dev/null @@ -1,36 +0,0 @@ -Changes in module 'nf-core/samtools/view' ---- modules/nf-core/samtools/view/main.nf -+++ modules/nf-core/samtools/view/main.nf -@@ -13,13 +13,14 @@ - path qname - - output: -- tuple val(meta), path("*.bam"), emit: bam, optional: true -- tuple val(meta), path("*.cram"), emit: cram, optional: true -- tuple val(meta), path("*.sam"), emit: sam, optional: true -- tuple val(meta), path("*.bai"), emit: bai, optional: true -- tuple val(meta), path("*.csi"), emit: csi, optional: true -- tuple val(meta), path("*.crai"), emit: crai, optional: true -- path "versions.yml", emit: versions -+ tuple val(meta), path("*.bam"), emit: bam, optional: true -+ tuple val(meta), path("*.cram"), emit: cram, optional: true -+ tuple val(meta), path("*.sam"), emit: sam, optional: true -+ tuple val(meta), path("*.bai"), emit: bai, optional: true -+ tuple val(meta), path("*.csi"), emit: csi, optional: true -+ tuple val(meta), path("*.crai"), emit: crai, optional: true -+ tuple val(meta), path("*.unoutput"), emit: unoutput, optional: true -+ path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when -@@ -29,7 +30,7 @@ - def args2 = task.ext.args2 ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def reference = fasta ? "--reference ${fasta}" : "" -- def readnames = qname ? "--qname-file ${qname}": "" -+ def readnames = qname ? "--qname-file ${qname} --unoutput ${prefix}.unoutput": "" - def file_type = args.contains("--output-fmt sam") ? "sam" : - args.contains("--output-fmt bam") ? "bam" : - args.contains("--output-fmt cram") ? "cram" : - -************************************************************