From 606ffc0eb1a7385c2aaea4b4d3ebc5dbe721614c Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 20 Jan 2023 13:40:59 +0100 Subject: [PATCH 1/2] Remove platform specificity for MALT --- subworkflows/local/profiling.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index 6613648..4b4952c 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -67,7 +67,6 @@ workflow PROFILING { // 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 ch_input_for_malt = ch_input_for_profiling.malt - .filter { it[0]['instrument_platform'] == 'ILLUMINA' } .map { meta, reads, db_meta, db -> From 2439aa69d0195ca9a72893c8e4b0dc1a3112d243 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 24 Jan 2023 10:58:03 +0100 Subject: [PATCH 2/2] Use specific samplesheet for MALT without LR reads due to GHA memory limits --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a26c28b..ea98e78 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -169,5 +169,5 @@ jobs: - name: Run pipeline with test data uses: Wandalen/wretry.action@v1.0.11 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