From 47e18a0a250545777e53f2a6ec6a3a915f6886ec Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 20 Apr 2021 13:10:15 +0200 Subject: [PATCH 1/3] Update main.nf --- main.nf | 24 ++++++------------------ 1 file changed, 6 insertions(+), 18 deletions(-) diff --git a/main.nf b/main.nf index 6033028c6..005221499 100644 --- a/main.nf +++ b/main.nf @@ -791,9 +791,7 @@ process adapter_removal { mv *.settings output/ ## Add R_ and L_ for unmerged reads for DeDup compatibility - AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq - - pigz -p ${task.cpus} output/${base}.pe.combined.fq + AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq """ //PE mode, collapse and trim, outputting all reads, preserving 5p } else if (seqtype == 'PE' && !params.skip_collapse && !params.skip_trim && !params.mergedonly && params.preserve5p) { @@ -807,9 +805,7 @@ process adapter_removal { mv *.settings output/ ## Add R_ and L_ for unmerged reads for DeDup compatibility - AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq - - pigz -p ${task.cpus} output/${base}.pe.combined.fq + AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq """ // PE mode, collapse and trim but only output collapsed reads } else if ( seqtype == 'PE' && !params.skip_collapse && !params.skip_trim && params.mergedonly && !params.preserve5p ) { @@ -820,9 +816,7 @@ process adapter_removal { cat *.collapsed.gz *.collapsed.truncated.gz > output/${base}.pe.combined.tmp.fq.gz ## Add R_ and L_ for unmerged reads for DeDup compatibility - AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq - - pigz -p ${task.cpus} output/${base}.pe.combined.fq + AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq mv *.settings output/ """ @@ -835,9 +829,7 @@ process adapter_removal { cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz ## Add R_ and L_ for unmerged reads for DeDup compatibility - AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq - - pigz -p ${task.cpus} output/${base}.pe.combined.fq + AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq mv *.settings output/ """ @@ -851,9 +843,7 @@ process adapter_removal { cat *.collapsed.gz *.pair1.truncated.gz *.pair2.truncated.gz > output/${base}.pe.combined.tmp.fq.gz ## Add R_ and L_ for unmerged reads for DeDup compatibility - AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq - - pigz -p ${task.cpus} output/${base}.pe.combined.fq + AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq mv *.settings output/ """ @@ -867,9 +857,7 @@ process adapter_removal { cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz ## Add R_ and L_ for unmerged reads for DeDup compatibility - AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq - - pigz -p ${task.cpus} output/${base}.pe.combined.fq + AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq mv *.settings output/ """ From ad448fe60e2cf41343be5bcb3ff3c3ee38f7a441 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 20 Apr 2021 13:28:35 +0200 Subject: [PATCH 2/3] Update main.nf --- main.nf | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/main.nf b/main.nf index 005221499..10de222d4 100644 --- a/main.nf +++ b/main.nf @@ -791,7 +791,7 @@ process adapter_removal { mv *.settings output/ ## Add R_ and L_ for unmerged reads for DeDup compatibility - AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq + AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq.gz """ //PE mode, collapse and trim, outputting all reads, preserving 5p } else if (seqtype == 'PE' && !params.skip_collapse && !params.skip_trim && !params.mergedonly && params.preserve5p) { @@ -805,7 +805,7 @@ process adapter_removal { mv *.settings output/ ## Add R_ and L_ for unmerged reads for DeDup compatibility - AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq + AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq.gz """ // PE mode, collapse and trim but only output collapsed reads } else if ( seqtype == 'PE' && !params.skip_collapse && !params.skip_trim && params.mergedonly && !params.preserve5p ) { @@ -816,7 +816,7 @@ process adapter_removal { cat *.collapsed.gz *.collapsed.truncated.gz > output/${base}.pe.combined.tmp.fq.gz ## Add R_ and L_ for unmerged reads for DeDup compatibility - AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq + AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq.gz mv *.settings output/ """ @@ -829,7 +829,7 @@ process adapter_removal { cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz ## Add R_ and L_ for unmerged reads for DeDup compatibility - AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq + AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq.gz mv *.settings output/ """ @@ -843,7 +843,7 @@ process adapter_removal { cat *.collapsed.gz *.pair1.truncated.gz *.pair2.truncated.gz > output/${base}.pe.combined.tmp.fq.gz ## Add R_ and L_ for unmerged reads for DeDup compatibility - AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq + AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq.gz mv *.settings output/ """ @@ -857,7 +857,7 @@ process adapter_removal { cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz ## Add R_ and L_ for unmerged reads for DeDup compatibility - AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq + AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq.gz mv *.settings output/ """ From 28ac4e4ccba12a271f3e572bb13a01a9e2e4d74d Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sun, 25 Apr 2021 16:55:11 +0200 Subject: [PATCH 3/3] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0c107de7c..162bbc0bf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` +- Re-adds gzip piping to AdapterRemovalFixPrefix to speed up process after reports of being very slow + ### `Dependencies` - Removed pinning of `tbb` (upstream bug in bioconda fixed)