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Fix bug in getting software version for PycoQC process #213

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merged 3 commits into from
Jun 28, 2021
Merged

Fix bug in getting software version for PycoQC process #213

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81bdf6f
Fix bug in getting software version for PycoQC process
drpatelh Jun 28, 2021
3abc198
Initialise empty channel for PycoQC
drpatelh Jun 28, 2021
0a790c8
Upddate CHANGELOG
drpatelh Jun 28, 2021
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ jobs:
--input false,
--min_barcode_reads 10000,
--min_guppyplex_reads 10000,
"--artic_minion_caller medaka",
"--artic_minion_caller medaka --sequencing_summary false --fast5_dir false",
]
steps:
- name: Check out pipeline code
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements & fixes

* [[#212](https://github.com/nf-core/viralrecon/issues/212)] - Access to `PYCOQC.out` is undefined

### Parameters

## [[2.1](https://github.com/nf-core/rnaseq/releases/tag/2.1)] - 2021-06-15
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6 changes: 4 additions & 2 deletions workflows/nanopore.nf
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Expand Up @@ -127,12 +127,14 @@ workflow NANOPORE {
//
// MODULE: PycoQC on sequencing summary file
//
ch_pycoqc_multiqc = Channel.empty()
if (params.sequencing_summary && !params.skip_pycoqc) {
PYCOQC (
ch_sequencing_summary
)
ch_pycoqc_multiqc = PYCOQC.out.json
ch_software_versions = ch_software_versions.mix(PYCOQC.out.version.ifEmpty(null))
}
ch_software_versions = ch_software_versions.mix(PYCOQC.out.version.ifEmpty(null))

//
// SUBWORKFLOW: Uncompress and prepare reference genome files
Expand Down Expand Up @@ -506,7 +508,7 @@ workflow NANOPORE {
MULTIQC_CUSTOM_TSV_BARCODE_COUNT.out.ifEmpty([]),
MULTIQC_CUSTOM_TSV_GUPPYPLEX_COUNT.out.ifEmpty([]),
ch_amplicon_heatmap_multiqc.ifEmpty([]),
PYCOQC.out.json.collect().ifEmpty([]),
ch_pycoqc_multiqc.collect().ifEmpty([]),
ARTIC_MINION.out.json.collect{it[1]}.ifEmpty([]),
FILTER_BAM_SAMTOOLS.out.flagstat.collect{it[1]}.ifEmpty([]),
BCFTOOLS_STATS.out.stats.collect{it[1]}.ifEmpty([]),
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