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quantms 0.0.10 -> 0.0.11 #419

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merged 9 commits into from
Sep 11, 2024
Merged

quantms 0.0.10 -> 0.0.11 #419

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48622b8
Merge pull request #405 from bigbio/dev
ypriverol Aug 29, 2024
f8fa8e3
quantms-utils 0.0.10 -> 0.0.11
ypriverol Sep 10, 2024
0c0c811
Merge branch 'dev' of https://github.com/bigbio/quantms into dev
ypriverol Sep 10, 2024
195beaa
Merge branch 'master' of https://github.com/bigbio/quantms into dev
ypriverol Sep 10, 2024
9e42ec8
actions/upload-artifact@v1 -> v2
ypriverol Sep 10, 2024
95b1cff
actions/upload-artifact@v2 -> v4
ypriverol Sep 10, 2024
1b373be
actions/upload-artifact@v2 -> v4
ypriverol Sep 10, 2024
912a545
actions/upload-artifact@v2 -> v4
ypriverol Sep 10, 2024
a426e07
actions/upload-artifact@v2 -> v4
ypriverol Sep 10, 2024
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12 changes: 6 additions & 6 deletions .github/workflows/ci.yml
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Expand Up @@ -105,21 +105,21 @@ jobs:
mkdir failed_logs
failed=$(grep "FAILED" ${TEST_PROFILE}_${EXEC_PROFILE}_results/pipeline_info/execution_trace.txt | cut -f 2)
while read -r line ; do cp $(ls work/${line}*/*.log) failed_logs/ | true ; done <<< "$failed"
- uses: actions/upload-artifact@v1
- uses: actions/upload-artifact@v4
if: failure() || cancelled()
name: Upload failed logs
with:
name: failed_logs
name: failed_logs_${{ env.TEST_PROFILE }}_${{ env.EXEC_PROFILE }}_${{ github.run_id }}
path: failed_logs
- uses: actions/upload-artifact@v1
- uses: actions/upload-artifact@v4
if: always()
name: Upload results
with:
name: ${{ env.TEST_PROFILE }}_${{ env.EXEC_PROFILE }}_results
name: ${{ env.TEST_PROFILE }}_${{ env.EXEC_PROFILE }}_${{ github.run_id }}_results
path: ${{ env.TEST_PROFILE }}_${{ env.EXEC_PROFILE }}_results
- uses: actions/upload-artifact@v1
- uses: actions/upload-artifact@v4
if: always()
name: Upload log
with:
name: nextflow.log
name: nextflow_${{ env.TEST_PROFILE }}_${{ env.EXEC_PROFILE }}_${{ github.run_id }}.log
path: .nextflow.log
6 changes: 3 additions & 3 deletions modules/local/add_sage_feat/main.nf
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Expand Up @@ -2,10 +2,10 @@ process SAGEFEATURE {
tag "$meta.mzml_id"
label 'process_low'

conda "bioconda::quantms-utils=0.0.10"
conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.10--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.10--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"

input:
tuple val(meta), path(id_file), path(extra_feat)
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6 changes: 3 additions & 3 deletions modules/local/diannconvert/main.nf
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Expand Up @@ -2,10 +2,10 @@ process DIANNCONVERT {
tag "$meta.experiment_id"
label 'process_medium'

conda "bioconda::quantms-utils=0.0.10"
conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.10--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.10--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"

input:
path(report)
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6 changes: 3 additions & 3 deletions modules/local/extract_psm/main.nf
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Expand Up @@ -2,10 +2,10 @@ process PSMCONVERSION {
tag "$meta.mzml_id"
label 'process_medium'

conda "bioconda::quantms-utils=0.0.10"
conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.10--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.10--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"


input:
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6 changes: 3 additions & 3 deletions modules/local/extract_sample/main.nf
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Expand Up @@ -2,10 +2,10 @@ process GETSAMPLE {
tag "$design.Name"
label 'process_low'

conda "bioconda::quantms-utils=0.0.10"
conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.10--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.10--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"


input:
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6 changes: 3 additions & 3 deletions modules/local/generate_diann_cfg/main.nf
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Expand Up @@ -2,10 +2,10 @@ process GENERATE_DIANN_CFG {
tag "$meta.experiment_id"
label 'process_low'

conda "bioconda::quantms-utils=0.0.10"
conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.10--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.10--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"

input:
val(meta)
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6 changes: 3 additions & 3 deletions modules/local/ms2rescore/main.nf
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Expand Up @@ -2,10 +2,10 @@ process MS2RESCORE {
tag "$meta.mzml_id"
label 'process_high'

conda "bioconda::quantms-utils=0.0.10"
conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.10--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.10--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"

// userEmulation settings when docker is specified
containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : ''
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6 changes: 3 additions & 3 deletions modules/local/mzmlstatistics/main.nf
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Expand Up @@ -3,10 +3,10 @@ process MZMLSTATISTICS {
label 'process_medium'
label 'process_single'

conda "bioconda::quantms-utils=0.0.10"
conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.10--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.10--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"

input:
tuple val(meta), path(ms_file)
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6 changes: 3 additions & 3 deletions modules/local/preprocess_expdesign.nf
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Expand Up @@ -6,10 +6,10 @@ process PREPROCESS_EXPDESIGN {
tag "$design.Name"
label 'process_low'

conda "bioconda::quantms-utils=0.0.10"
conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.10--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.10--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"

input:
path design
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6 changes: 3 additions & 3 deletions modules/local/samplesheet_check.nf
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Expand Up @@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK {
tag "$input_file"
label 'process_single'

conda "bioconda::quantms-utils=0.0.10"
conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.10--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.10--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"

input:
path input_file
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6 changes: 3 additions & 3 deletions modules/local/sdrfparsing/main.nf
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Expand Up @@ -2,10 +2,10 @@ process SDRFPARSING {
tag "$sdrf.Name"
label 'process_low'

conda "bioconda::quantms-utils=0.0.10"
conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.10--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.10--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"

input:
path sdrf
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6 changes: 3 additions & 3 deletions modules/local/spectrum2features/main.nf
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Expand Up @@ -2,10 +2,10 @@ process SPECTRUM2FEATURES {
tag "$meta.mzml_id"
label 'process_low'

conda "bioconda::quantms-utils=0.0.10"
conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.10--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.10--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"

input:
tuple val(meta), path(id_file), path(ms_file)
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -492,7 +492,7 @@ manifest {
description = """Quantitative Mass Spectrometry nf-core workflow"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.3.0dev'
version = '1.3.1dev'
doi = '10.5281/zenodo.7754148'
}

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