Meta annotation now working (c7036de5) · Commits · Chaos / Cutandrun

conf/modules.config

+33 −51

Original line number	Diff line number	Diff line
		@@ -390,78 +390,60 @@ if(params.run_remove_dups) {
		}
		}

		/*
		========================================================================================
		ANNOTATE META WITH ALIGN AND DUP STATS
		========================================================================================
		*/

		// "picard_dedup" {
		// args = "-ASSUME_SORT_ORDER coordinate -REMOVE_DUPLICATES true -VALIDATION_STRINGENCY LENIENT -TMP_DIR tmp"
		// suffix = ".target.dedup"
		// publish_files = false
		// }
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:ANNOTATE_BT2_META:AWK_SCRIPT' {
		ext.suffix = ".target"
		publishDir = [
		enabled: false
		]
		}

		// "picard_dedup_samtools" {
		// suffix = ".target.dedup"
		// publish_files = false
		// }
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:ANNOTATE_BT2_SPIKEIN_META:AWK_SCRIPT' {
		ext.suffix = ".dedup"
		publishDir = [
		enabled: false
		]
		}

		// picard_deduplicates_options = modules["picard_dedup"]
		// picard_deduplicates_samtools_options = modules["picard_dedup_samtools"]
		// if(run_remove_dups) {
		// picard_deduplicates_options.publish_dir = "02_alignment/${params.aligner}/target/dedup"
		// picard_deduplicates_options.publish_files = ["bam":"","metrics.txt": "picard_metrics"]
		// picard_deduplicates_samtools_options.publish_dir = "02_alignment/${params.aligner}/target/dedup"
		// picard_deduplicates_samtools_options.publish_files = ["bai":"","stats":"samtools_stats", "flagstat":"samtools_stats", "idxstats":"samtools_stats"]
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:ANNOTATE_DEDUP_META:AWK' {
		ext.suffix = ".awk"
		ext.command = "'/^[^#]/{print}'"
		ext.command2 = " > int1.txt && head -2 int1.txt > int2.txt && sed 's/\\t/,/g' int2.txt > int3.txt && sed 's/.*/\\L&/g' int3.txt "
		publishDir = [
		enabled: false
		]
		}
		}

		// if(dedup_control_only) {
		// picard_markduplicates_options.publish_dir = "02_alignment/${params.aligner}/target/markdup"
		// picard_markduplicates_options.publish_files = ["bam":"","metrics.txt":"picard_metrics"]
		// picard_markduplicates_samtools_options.publish_dir = "02_alignment/${params.aligner}/target/markdup"
		// picard_markduplicates_samtools_options.publish_files = ["bai":"","stats":"samtools_stats", "flagstat":"samtools_stats", "idxstats":"samtools_stats"]
		// }
		// }
		// else if(params.save_align_intermed) {
		// picard_deduplicates_options.publish_dir = "02_alignment/${params.aligner}/target/intermed/dedup"
		// picard_deduplicates_options.publish_files = ["bam":"","metrics.txt":"picard_metrics"]
		// picard_deduplicates_samtools_options.publish_dir = "02_alignment/${params.aligner}/target/intermed/dedup"
		// picard_deduplicates_samtools_options.publish_files = ["bai":"","stats":"samtools_stats", "flagstat":"samtools_stats", "idxstats":"samtools_stats"]
		// }




		// //TODO: PEAK PLOTTING options - infact all reporting options - how t






		// //TODO: PEAK PLOTTING options - infact all reporting options - how t










		// "awk_dedup" {
		// args = ""
		// suffix = ".awk"
		// publish_dir = false
		// command = "'/^[^#]/{print}'"
		// command2 = " > int1.txt && head -2 int1.txt > int2.txt && sed 's/\\t/,/g' int2.txt > int3.txt && sed 's/.*/\\L&/g' int3.txt "
		// publish_files = false
		// }

		// /*
		// ========================================================================================
		// ANNOTATE META WITH ALIGN
		// ========================================================================================
		// */

		// "awk_bt2" {
		// suffix = ".target"
		// publish_files = false
		// }
		// "awk_bt2_spikein" {
		// suffix = ".spikein"
		// publish_files = false
		// }

		// /*
		// ========================================================================================

modules/local/linux/awk.nf

+3 −3

Original line number	Diff line number	Diff line
		@@ -4,8 +4,8 @@ process AWK {

		conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
		'quay.io/biocontainers/biocontainers:v1.2.0_cv1' }"
		'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
		'quay.io/biocontainers/gawk:5.1.0' }"

		input:
		tuple val(meta), path(input)
		@@ -29,7 +29,7 @@ process AWK {

		cat <<-END_VERSIONS > versions.yml
		"${task.process}":
		awk: \$(awk -W version \| head -n 1 \| egrep -o "([0-9]{1,}\\.)+[0-9]{1,}")
		awk: \$(awk -Wversion 2>/dev/null \| head -n 1 \| awk '{split(\$0,a,","); print a[1];}' \| egrep -o "([0-9]{1,}\\.)+[0-9]{1,}")
		END_VERSIONS
		"""
		}

modules/local/linux/awk_script.nf

+3 −3

Original line number	Diff line number	Diff line
		@@ -4,8 +4,8 @@ process AWK_SCRIPT {

		conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
		'quay.io/biocontainers/biocontainers:v1.2.0_cv1' }"
		'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
		'quay.io/biocontainers/gawk:5.1.0' }"

		input:
		tuple val(meta), path(input)
		@@ -26,7 +26,7 @@ process AWK_SCRIPT {

		cat <<-END_VERSIONS > versions.yml
		"${task.process}":
		awk: \$(awk -W version \| head -n 1 \| egrep -o "([0-9]{1,}\\.)+[0-9]{1,}")
		awk: \$(awk -Wversion 2>/dev/null \| head -n 1 \| awk '{split(\$0,a,","); print a[1];}' \| egrep -o "([0-9]{1,}\\.)+[0-9]{1,}")
		END_VERSIONS
		"""
		}

modules/local/linux/cut.nf

+3 −3

Original line number	Diff line number	Diff line
		@@ -2,10 +2,10 @@ process CUT {
		tag "$meta.id"
		label 'process_low'

		conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
		conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
		'quay.io/biocontainers/biocontainers:v1.2.0_cv1' }"
		'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
		'quay.io/biocontainers/gawk:5.1.0' }"

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

modules/local/linux/sort.nf

+3 −3

Original line number	Diff line number	Diff line
		@@ -2,10 +2,10 @@ process SORT {
		tag "$meta.id"
		label 'process_medium'

		conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
		conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
		'quay.io/biocontainers/biocontainers:v1.2.0_cv1' }"
		'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
		'quay.io/biocontainers/gawk:5.1.0' }"

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

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