Merge branch 'nf-core:master' into maxquant

This commit is contained in:
Veit Schwämmle 2022-01-21 08:55:28 +01:00 committed by GitHub
commit 4ba69d20fc
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4 changed files with 23 additions and 19 deletions

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@ -48,11 +48,6 @@ jobs:
restore-keys: |
${{ runner.os }}-pip-
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install Python dependencies
run: python -m pip install --upgrade pip pytest-workflow
@ -93,6 +88,16 @@ jobs:
# only use one thread for pytest-workflow to avoid race condition on conda cache.
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
- name: Output log on failure
if: failure()
run: |
echo "======> log.out <======="
cat /home/runner/pytest_workflow_*/*/log.out
echo
echo
echo "======> log.err <======="
cat /home/runner/pytest_workflow_*/*/log.err
- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v2

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@ -1,13 +1,11 @@
def VERSION = '0.1' // Version information not provided by tool on CLI
process CHROMAP_CHROMAP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::chromap=0.1 bioconda::samtools=1.13" : null)
conda (params.enable_conda ? "bioconda::chromap=0.1.5 bioconda::samtools=1.14" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' :
'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' :
'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' }"
input:
tuple val(meta), path(reads)
@ -45,7 +43,7 @@ process CHROMAP_CHROMAP {
args_list << "--pairs-natural-chr-order $pairs_chr_order"
}
def final_args = args_list.join(' ')
def compression_cmds = "gzip ${prefix}.${file_extension}"
def compression_cmds = "gzip -n ${prefix}.${file_extension}"
if (args.contains("--SAM")) {
compression_cmds = """
samtools view $args2 -@ $task.cpus -bh \\
@ -67,7 +65,8 @@ process CHROMAP_CHROMAP {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
chromap: $VERSION
chromap: \$(echo \$(chromap --version 2>&1))
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
} else {
@ -85,7 +84,8 @@ process CHROMAP_CHROMAP {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
chromap: $VERSION
chromap: \$(echo \$(chromap --version 2>&1))
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}

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@ -5,9 +5,8 @@
- chromap
files:
- path: output/chromap/genome.index
md5sum: f889d5f61d80823766af33277d27d386
- path: output/chromap/test.bed.gz
md5sum: 7029066c27ac6f5ef18d660d5741979a
md5sum: 25e40bde24c7b447292cd68573728694
- name: chromap chromap test_chromap_chromap_paired_end
command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@ -16,9 +15,8 @@
- chromap
files:
- path: output/chromap/genome.index
md5sum: f889d5f61d80823766af33277d27d386
- path: output/chromap/test.bed.gz
md5sum: cafd8fb21977f5ae69e9008b220ab169
md5sum: 7cdc8448882b75811e0c784f5f20aef2
- name: chromap chromap test_chromap_chromap_paired_bam
command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@ -27,6 +25,5 @@
- chromap
files:
- path: output/chromap/genome.index
md5sum: f889d5f61d80823766af33277d27d386
- path: output/chromap/test.bam
md5sum: bd1e3fe0f3abd1430ae191754f16a3ed
md5sum: 73e2c76007e3c61df625668e01b3f42f

View file

@ -5,3 +5,5 @@
- chromap
files:
- path: output/chromap/genome.index