Updated modules (a0ae06d1) · Commits · Chaos / Cutandrun

modules.json

+12 −12

Original line number	Diff line number	Diff line
		@@ -4,28 +4,28 @@
		"repos": {
		"nf-core/modules": {
		"bedtools/bamtobed": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"bedtools/genomecov": {
		"git_sha": "e8b33e6eb1be2a03abdd2c06068f9a5cebc02bb4"
		},
		"bedtools/intersect": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"bedtools/merge": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"bedtools/sort": {
		"git_sha": "2959b4ba070d138d1577acc48d35cc669fbef972"
		},
		"bowtie2/align": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"bowtie2/build": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"cat/fastq": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"deeptools/computematrix": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		@@ -34,31 +34,31 @@
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"fastqc": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"gunzip": {
		"git_sha": "e560fbbc3ed68e62bc810a50f552394056f81762"
		},
		"picard/markduplicates": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"samtools/flagstat": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"samtools/idxstats": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"samtools/index": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"samtools/sort": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"samtools/stats": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"samtools/view": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "ac1e6df076195cec553a2079c9cebd94026a0d47"
		},
		"seacr/callpeak": {
		"git_sha": "4d89d6b2f0c478ac7ef80ece5cad44fdf7ffd614"
		@@ -70,7 +70,7 @@
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"untar": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		}
		}
		}

modules/nf-core/modules/samtools/view/main.nf

+8 −4

Original line number	Diff line number	Diff line
		@@ -19,16 +19,20 @@ process SAMTOOLS_VIEW {
		}

		input:
		tuple val(meta), path(bam)
		tuple val(meta), path(input)
		path fasta

		output:
		tuple val(meta), path("*.bam"), emit: bam
		tuple val(meta), path("*.bam") , optional: true, emit: bam
		tuple val(meta), path("*.cram"), optional: true, emit: cram
		path "versions.yml" , emit: versions

		script:
		def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
		def reference = fasta ? "--reference ${fasta} -C" : ""
		def file_type = input.getExtension()
		"""
		samtools view $options.args $bam > ${prefix}.bam
		samtools view ${reference} $options.args $input > ${prefix}.${file_type}
		cat <<-END_VERSIONS > versions.yml
		${getProcessName(task.process)}:
		${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) \| sed 's/^.samtools //; s/Using.\$//')

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