fix: addresssing incompatibility with snakemake>=8.0.0

OpenOmics · Feb 8, 2024 · f50e75c · f50e75c
1 parent 7ba731a
commit f50e75c
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git 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
@@ -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:
         """