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Updated NCBI FCS GX to 0.5.4 #101

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Jul 19, 2024
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Updated NCBI FCS GX to 0.5.4 #101

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4 changes: 3 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -14,7 +14,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

1. Fixed a bug where `intron_length_distribution` was used instead of `cds_length_distribution` when creating the CDS Length Distribution Graph [#95](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/95)
2. Fixed a bug where 'Subsequent pipeline modules are skipped.' was printed in the `report.html` even when `contamination_stops_pipeline` was set to false
3. Changed default branch name from `master` to `main` in nf-core template files
3. Updated NCBI FCS GX to 0.5.4 [#93](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/93)
4. Now NCBI FCS GX module uses all the cores available from the Nextflow task
5. Changed default branch name from `master` to `main` in nf-core template files

### `Dependencies`

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20 changes: 14 additions & 6 deletions modules/local/ncbi_fcs_gx_screen_samples.nf
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Expand Up @@ -2,10 +2,10 @@ process NCBI_FCS_GX_SCREEN_SAMPLES {
tag 'all samples'
label 'process_high'

conda "bioconda::ncbi-fcs-gx=0.5.0"
conda "bioconda::ncbi-fcs-gx=0.5.4"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ncbi-fcs-gx:0.5.0--h4ac6f70_3':
'biocontainers/ncbi-fcs-gx:0.5.0--h4ac6f70_3' }"
'https://depot.galaxyproject.org/singularity/ncbi-fcs-gx:0.5.4--h4ac6f70_0':
'biocontainers/ncbi-fcs-gx:0.5.4--h4ac6f70_0' }"

input:
path samples
Expand All @@ -21,12 +21,20 @@ process NCBI_FCS_GX_SCREEN_SAMPLES {
task.ext.when == null || task.ext.when

script:
def VERSION = 0.5
def VERSION = '0.5.4'
"""
export GX_NUM_CORES=$task.cpus

for sample_fasta in $samples;
do
sample_tag=\$(echo "\$sample_fasta" | sed 's/fasta.file.for.//g' | sed 's/.fasta//g')
run_gx.py --fasta ./\$sample_fasta --out-dir ./ --gx-db $db_path --tax-id "${tax_id}"

run_gx.py \\
--fasta ./\$sample_fasta \\
--out-dir ./ \\
--gx-db $db_path \\
--tax-id "${tax_id}" \\
--phone-home-label github/$workflow.manifest.name

mv "\${sample_fasta%.fasta}.${tax_id}.fcs_gx_report.txt" "\${sample_tag}.fcs_gx_report.txt"
mv "\${sample_fasta%.fasta}.${tax_id}.taxonomy.rpt" "\${sample_tag}.taxonomy.rpt"
Expand All @@ -39,7 +47,7 @@ process NCBI_FCS_GX_SCREEN_SAMPLES {
"""

stub:
def VERSION = 0.5
def VERSION = '0.5.4'
"""
for sample_fasta in $samples;
do
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