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Update modules required for rnaseq pipeline #449

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merged 8 commits into from
Apr 16, 2021
Merged

Update modules required for rnaseq pipeline #449

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7782f80
Update HISAT2 build module
drpatelh Apr 15, 2021
9e8b331
Bump preseq version
drpatelh Apr 15, 2021
12f20e5
Fix tests
drpatelh Apr 15, 2021
68d820a
Add meta.yml for preseq to fix linting
drpatelh Apr 15, 2021
cba41d8
Auto-detect --genomeSAindexNbases for smaller genomes
drpatelh Apr 15, 2021
1725d2f
Add placeholder to use human data for the tests
drpatelh Apr 15, 2021
1d97cd3
Add CSI output option to samtools/index
drpatelh Apr 15, 2021
cbdfaf0
Fix samtools/index tests
drpatelh Apr 15, 2021
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14 changes: 8 additions & 6 deletions software/hisat2/build/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ def VERSION = '2.2.0'
process HISAT2_BUILD {
tag "$fasta"
label 'process_high'
label 'process_high_memory'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
Expand All @@ -26,7 +27,7 @@ process HISAT2_BUILD {
path splicesites

output:
path "hisat2", emit: index
path "hisat2" , emit: index
path "*.version.txt", emit: version

script:
Expand All @@ -38,17 +39,18 @@ process HISAT2_BUILD {
avail_mem = task.memory.toGiga()
}

def extract_exons = ''
def ss = ''
def exon = ''
if (avail_mem > params.hisat_build_memory) {
log.info "[HISAT2 index build] Over ${params.hisat_build_memory} GB available, so using splice sites and exons in HISAT2 index"
def extract_exons = ''
def hisat2_build_memory = params.hisat2_build_memory ? (params.hisat2_build_memory as nextflow.util.MemoryUnit).toGiga() : 0
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if (avail_mem >= hisat2_build_memory) {
log.info "[HISAT2 index build] At least ${hisat2_build_memory} GB available, so using splice sites and exons to build HISAT2 index"
extract_exons = "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt"
ss = "--ss $splicesites"
exon = "--exon ${gtf.baseName}.exons.txt"
} else {
log.info "[HISAT2 index build] Less than ${params.hisat_build_memory} GB available, so NOT using splice sites and exons in HISAT2 index."
log.info "[HISAT2 index build] Use --hisat_build_memory [small number] to skip this check."
log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index."
log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check."
}

def software = getSoftwareName(task.process)
Expand Down
6 changes: 3 additions & 3 deletions software/preseq/lcextrap/main.nf
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Expand Up @@ -12,11 +12,11 @@ process PRESEQ_LCEXTRAP {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

conda (params.enable_conda ? "bioconda::preseq=2.0.3" : null)
conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/preseq:2.0.3--hf53bd2b_3"
container "https://depot.galaxyproject.org/singularity/preseq:3.1.2--h06ef8b0_1"
} else {
container "quay.io/biocontainers/preseq:2.0.3--hf53bd2b_3"
container "quay.io/biocontainers/preseq:3.1.2--h06ef8b0_1"
}

input:
Expand Down
4 changes: 2 additions & 2 deletions tests/software/preseq/lcextrap/test.yml
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Expand Up @@ -5,7 +5,7 @@
- preseq/lcextrap
files:
- path: output/preseq/test.ccurve.txt
md5sum: 76ae04c8eaf19c94e3210bb69da38498
md5sum: 1fa5cdd601079329618f61660bee00de
- path: output/preseq/test.command.log

- name: preseq lcextrap paired-end
Expand All @@ -15,5 +15,5 @@
- preseq/lcextrap
files:
- path: output/preseq/test.ccurve.txt
md5sum: 2836d2fabd2213f097fd7063db550276
md5sum: 10e5ea860e87fb6f5dc10f4f20c62040
- path: output/preseq/test.command.log