From f50e75cf63a1ebf54c5022e8ff197f29a97e4abb Mon Sep 17 00:00:00 2001 From: Ryan Routsong Date: Thu, 8 Feb 2024 14:46:38 -0500 Subject: [PATCH] fix: addresssing incompatibility with snakemake>=8.0.0 --- .github/workflows/dryrun.yaml | 4 ++-- workflow/qc.smk | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/dryrun.yaml b/.github/workflows/dryrun.yaml index 4e865d8..e69bc1c 100644 --- a/.github/workflows/dryrun.yaml +++ b/.github/workflows/dryrun.yaml @@ -14,7 +14,7 @@ jobs: - uses: docker://snakemake/snakemake:v7.32.4 - name: Dry Run with test data run: | - docker run -h cn0000 -v $PWD:/opt2 -w /opt2 snakemake/snakemake:stable /bin/bash -c \ + docker run -h cn0000 -v $PWD:/opt2 -w /opt2 snakemake/snakemake:v7.32.4 /bin/bash -c \ "source get_submods.sh; pip install -r requirements.txt; ./weave run --sheetname paired_end.csv -s /opt2/.tests/paired_end -o /opt2/.tests/dry_run_out --local --dry-run /opt2/.tests/paired_end" - name: View the pipeline config file run: | @@ -52,7 +52,7 @@ jobs: - uses: docker://snakemake/snakemake:v7.32.4 - name: Dry Run with test data run: | - docker run -h cn0000 -v $PWD:/opt2 -w /opt2 snakemake/snakemake:stable /bin/bash -c \ + docker run -h cn0000 -v $PWD:/opt2 -w /opt2 snakemake/snakemake:v7.32.4 /bin/bash -c \ "source get_submods.sh; pip install -r requirements.txt;./weave run --sheetname single_end.csv -s /opt2/.tests/single_end -o /opt2/.tests/dry_run_out --local --dry-run /opt2/.tests/single_end" - name: View the pipeline config file run: | diff --git a/workflow/qc.smk b/workflow/qc.smk index d067e4c..09b1b47 100644 --- a/workflow/qc.smk +++ b/workflow/qc.smk @@ -48,7 +48,7 @@ rule fastqc_trimmed: threads: 4 resources: mem_mb = 8096, - disk_mb = int(500e3) if config['use_scratch'] else 0, + disk_mb = int(500e3) if config.get('use_scratch', True) else 0, log: config['out_to'] + "/logs/" + config["project"] + "/fastqc_trimmed/{sids}_R{rnums}.log" shell: """