Support use_tmpdir; pbalign can use . as TMPDIR

PacificBiosciences/FALCON#651
pb-cdunn · Aug 2, 2018 · 94cbe11 · 94cbe11
1 parent f601e55
commit 94cbe11
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/falcon_unzip/tasks/unzip.py b/falcon_unzip/tasks/unzip.py
@@ -253,7 +253,7 @@
 date
 
 samtools faidx {input.ref_fasta}
-pbalign --tmpDir=/scratch/ --nproc=24 --minAccuracy=0.75 --minLength=50\
+pbalign --tmpDir=$(pwd)/tmp --nproc=24 --minAccuracy=0.75 --minLength=50\
           --minAnchorSize=12 --maxDivergence=30 --concordant --algorithm=blasr\
           --algorithmOptions=--useQuality --maxHits=1 --hitPolicy=random --seed=1\
             {input.read_bam} {input.ref_fasta} aln-{params.ctg_id}.bam
@@ -696,7 +696,6 @@ def run_workflow(wf, config, rule_writer):
             outputs={
                 'results': './4-quiver/quiver-run/{ctg_id}/results.json',
             },
-            parameters={},
         ),
         dist=Dist(NPROC=24,
             job_dict=config['job.step.unzip.quiver'],

diff --git a/falcon_unzip/unzip.py b/falcon_unzip/unzip.py
@@ -17,8 +17,11 @@
 
 
 def unzip_all(config):
+    job_defaults = config['job.defaults']
+    use_tmpdir = job_defaults['use_tmpdir'] # None/False is fine.
     wf = PypeProcWatcherWorkflow(
-        job_defaults=config['job.defaults'],
+        job_defaults=job_defaults,
+        use_tmpdir=use_tmpdir,
     )
     with open('foo.snake', 'w') as snakemake_writer:
         rule_writer = snakemake.SnakemakeRuleWriter(snakemake_writer)