Add back parallel trim step. Moved fastqc step after trim.
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- 5c9e24e4 - Update with set for since only 1 variable. Also update pattern to pass files.
343 341 344 342 output: 345 343 path ("*.fq.gz") into fastqsTrim 344 path ("*.fastq.gz") into fastqs_fastqc changed this line in version 4 of the diff
882 881 } 883 882 884 883 // Replicate rawBam for multiple process inputs 885 rawBam.into { 884 rawBam.set { changed this line in version 4 of the diff
113 113 - merge_requests 114 114 script: 115 115 - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --version > version_trimgalore.txt 116 - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz 117 - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F6_1M.pe ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz 116 - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz changed this line in version 4 of the diff
113 113 - merge_requests 114 114 script: 115 115 - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --version > version_trimgalore.txt 116 - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz 117 - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F6_1M.pe ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz 116 - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz 117 - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F6_1M.pe ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz changed this line in version 4 of the diff
9 9 * Make pull references from BioHPC default (including in biohpc.config) 10 10 * Start using new gudmaprbk dockerhub (images autobuilt) 11 11 * Moved consistency checks to be fully python 12 * Added back parallel form of trim_galore and now use fastqc after trim step changed this line in version 4 of the diff
mentioned in commit 83d47884
