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bump bclconvert version (#1806)

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Matthias De Smet 2022-06-24 07:14:42 +02:00 committed by GitHub
parent a7193dc628
commit 5e2325956c
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GPG key ID: 4AEE18F83AFDEB23
3 changed files with 5 additions and 5 deletions
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4
modules/bclconvert/main.nf
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@ -5,7 +5,7 @@ process BCLCONVERT {
if (params.enable_conda) { if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using bcl-convert. Please use docker or singularity containers." exit 1, "Conda environments cannot be used when using bcl-convert. Please use docker or singularity containers."
} }
container "nfcore/bclconvert:3.9.3" container "nfcore/bclconvert:3.10.5"
input: input:
tuple val(meta), path(samplesheet), path(run_dir) tuple val(meta), path(samplesheet), path(run_dir)
@ -13,7 +13,7 @@ process BCLCONVERT {
output: output:
tuple val(meta), path("**[!Undetermined]_S*_L00?_R?_00?.fastq.gz") ,emit: fastq tuple val(meta), path("**[!Undetermined]_S*_L00?_R?_00?.fastq.gz") ,emit: fastq
tuple val(meta), path("**_S*_L00?_I?_00?.fastq.gz") ,optional:true ,emit: fastq_idx tuple val(meta), path("**_S*_L00?_I?_00?.fastq.gz") ,optional:true ,emit: fastq_idx
tuple val(meta), path("Undetermined_S0_L00?_R?_00?.fastq.gz") ,emit: undetermined tuple val(meta), path("Undetermined_S0_L00?_R?_00?.fastq.gz") ,optional:true ,emit: undetermined
tuple val(meta), path("Undetermined_S0_L00?_I?_00?.fastq.gz") ,optional:true, emit: undetermined_idx tuple val(meta), path("Undetermined_S0_L00?_I?_00?.fastq.gz") ,optional:true, emit: undetermined_idx
tuple val(meta), path("Reports") ,emit: reports tuple val(meta), path("Reports") ,emit: reports
tuple val(meta), path("Logs") ,emit: logs tuple val(meta), path("Logs") ,emit: logs

2
modules/bclconvert/meta.yml
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@ -39,7 +39,7 @@ output:
pattern: "**_S*_L00?_I?_00?.fastq.gz" pattern: "**_S*_L00?_I?_00?.fastq.gz"
- undetermined: - undetermined:
type: file type: file
description: Undetermined sample FASTQ files description: Optional undetermined sample FASTQ files
pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz"
- undetermined_idx: - undetermined_idx:
type: file type: file

4
tests/modules/bclconvert/test.yml
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@ -10,7 +10,7 @@
- path: output/bclconvert/Reports/Adapter_Metrics.csv - path: output/bclconvert/Reports/Adapter_Metrics.csv
md5sum: 989240b8840b2169ac1061f952c90f6c md5sum: 989240b8840b2169ac1061f952c90f6c
- path: output/bclconvert/Reports/Demultiplex_Stats.csv - path: output/bclconvert/Reports/Demultiplex_Stats.csv
md5sum: bb2ed9c6b46e03fbc060efd2c75398b0 md5sum: 93949a8cd96f907d83e0808c1ec2a04b
- path: output/bclconvert/Reports/IndexMetricsOut.bin - path: output/bclconvert/Reports/IndexMetricsOut.bin
md5sum: 9e688c58a5487b8eaf69c9e1005ad0bf md5sum: 9e688c58a5487b8eaf69c9e1005ad0bf
- path: output/bclconvert/Reports/Index_Hopping_Counts.csv - path: output/bclconvert/Reports/Index_Hopping_Counts.csv
@ -26,7 +26,7 @@
- path: output/bclconvert/Reports/fastq_list.csv - path: output/bclconvert/Reports/fastq_list.csv
md5sum: 05bc84f51840f5754cfb8381b36f2cb0 md5sum: 05bc84f51840f5754cfb8381b36f2cb0
- path: output/bclconvert/Sample1_S1_L001_R1_001.fastq.gz - path: output/bclconvert/Sample1_S1_L001_R1_001.fastq.gz
md5sum: 883037281293a2ec4995d34257f19866 md5sum: 57d2f3b389656245f923351d3e3d2d65
- path: output/bclconvert/Undetermined_S0_L001_R1_001.fastq.gz - path: output/bclconvert/Undetermined_S0_L001_R1_001.fastq.gz
md5sum: a4745abc5e7fdb89cc6df3069f3c6e69 md5sum: a4745abc5e7fdb89cc6df3069f3c6e69
- path: output/bclconvert/flowcell/InterOp/ControlMetricsOut.bin - path: output/bclconvert/flowcell/InterOp/ControlMetricsOut.bin