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Merge pull request #215 from nf-core/remove-platform-specificity

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Remove platform specificity for MALT
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James A. Fellows Yates 2023-01-24 11:47:48 +01:00 committed by GitHub
commit 03ef6a69f8
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2 changed files with 1 additions and 2 deletions
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2
.github/workflows/ci.yml vendored
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@ -169,5 +169,5 @@ jobs:
- name: Run pipeline with test data - name: Run pipeline with test data
uses: Wandalen/wretry.action@v1.0.11 uses: Wandalen/wretry.action@v1.0.11
with: with:
command: nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --run_malt --outdir ./results command: nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --run_malt --input 'https://github.com/nf-core/test-datasets/raw/taxprofiler/samplesheet_shortreadsonly.csv' --outdir ./results
attempt_limit: 3 attempt_limit: 3

1
subworkflows/local/profiling.nf
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@ -67,7 +67,6 @@ workflow PROFILING {
// MALT: We groupTuple to have all samples in one channel for MALT as database // MALT: We groupTuple to have all samples in one channel for MALT as database
// loading takes a long time, so we only want to run it once per database // loading takes a long time, so we only want to run it once per database
ch_input_for_malt = ch_input_for_profiling.malt ch_input_for_malt = ch_input_for_profiling.malt
.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
.map { .map {
meta, reads, db_meta, db -> meta, reads, db_meta, db ->