fix: correct github action issues with escape and snakemake args

OpenOmics · Feb 8, 2024 · dce0ff9 · dce0ff9
1 parent 606b446
commit dce0ff9
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Showing 5 changed files with 9 additions and 145 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,6 @@
 logs
-**.tests/illumnia_demux/dry_run_out
 .snakemake
 site
 output
-**.tests/dry_run_out
+.tests/illumnia_demux/dry_run_out
+.tests/dry_run_out
diff --git a/.tests/dry_run_out/paired_end/.config/config_job_0.json b/.tests/dry_run_out/paired_end/.config/config_job_0.json
diff --git a/scripts/utils.py b/scripts/utils.py
@@ -221,7 +221,7 @@ def get_mounts(*extras):
             file_to, file_from, mode = str(bind), str(bind), 'rw'
         mounts.append(file_from + ':' + file_to + ':' + mode)
 
-    mounts.append('\$TMPDIR:/tmp:rw')
+    mounts.append(r'\$TMPDIR:/tmp:rw')
 
     return ','.join(mounts)
 
@@ -266,7 +266,7 @@ def exec_pipeline(configs, dry_run=False, local=False):
         top_env['SNK_CONFIG'] = str(config_file.absolute())
         top_env['SINGULARITY_CACHEDIR'] = str(Path(this_config['out_to'], '.singularity').absolute())
         this_cmd = [
-            "snakemake", "-pr",
+            "snakemake", "-p", "-r",
             "--use-singularity",
             "--rerun-incomplete",
             "--keep-incomplete",

diff --git a/utils b/utils
diff --git a/workflow/qc.smk b/workflow/qc.smk
@@ -43,12 +43,12 @@ rule fastqc_trimmed:
         fqreport      = config['out_to'] + "/" + config["project"] + "/{sids}/fastqc_trimmed/{sids}_trimmed_R{rnums}_fastqc.zip",
     params:
         output_dir    = lambda w: config['out_to'] + "/" + config["project"] + "/" + w.sids + "/fastqc_trimmed/",
+        tmpdir        = lambda wc: '/tmp/' + wc.sids,
     containerized: config["resources"]["sif"] + "weave_ngsqc_0.0.2.sif"
     threads: 4
     resources: 
-        mem_mb = 8096,
-        disk_mb = int(500e3) if config['use_scratch'] else 0,
-        tmpdir = lambda wc: '/tmp/' + wc.sids,
+        mem_mb        = 8096,
+        disk_mb       = int(500e3) if config['use_scratch'] else 0,
     log: config['out_to'] + "/logs/" + config["project"] + "/fastqc_trimmed/{sids}_R{rnums}.log"
     shell:
         """
@@ -74,7 +74,7 @@ rule fastqc_trimmed:
         find "${{tmp}}" \\
             -type f \\
             \\( -name '*.html' -o -name '*.zip' \\) \\
-            -exec cp {{}} {params.outdir} \\;
+            -exec cp {{}} {params.output_dir} \\;
         """