more formatting fixes and debugging

Signed-off-by: vsoch <vsochat@stanford.edu>

bio/benchmark/chm-eval-sample/wrapper.py

@@ -18,10 +18,10 @@
     pipefail = "set +o pipefail"
 
     os.system(
-        f'/bin/bash -c "{pipefail} '
+        f"{pipefail} "
         f"samtools view {fmt} {url} {prefix} > {snakemake.output.bam} "
         f"samtools index {snakemake.output.bam} "
-        f'{log}"'
+        f"{log}"
     )
 else:
     os.system(

bio/bismark/bismark2report/wrapper.py

@@ -53,13 +53,13 @@ def answer2bool(v):
 skip_optional_reports = answer2bool(
     snakemake.params.get("skip_optional_reports", False)
 )
+
 for report_name in reports:
     path = snakemake.input.get(report_name, "")
     if path:
-        locals()[report_name] = path
-        cmds.append("--{0} {{{1}}}".format(report_name, report_name))
+        cmds.append("--%s %s" % (report_name, path))
     elif skip_optional_reports:
-        cmds.append("--{0} 'none'".format(report_name))
+        cmds.append("--%s 'none'" % report_name)
 
 # log
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)

bio/bwa/samse/wrapper.py

@@ -6,6 +6,7 @@
 __license__ = "MIT"
 
 
+import os
 from os import path
 
 
@@ -50,10 +51,10 @@
 
 # Run command.
 os.system(
-    f"(bwa samse"
+    f'/bin/bash -c "(bwa samse'
     f" {extra}"
     f" {snakemake.params.index}"
     f" {snakemake.input.sai}"
     f" {snakemake.input.fastq}"
-    f" | " + pipe_cmd + f") {log}"
+    f" | " + pipe_cmd + f') {log}"'
 )

bio/fgbio/filterconsensusreads/wrapper.py

@@ -21,7 +21,7 @@
     )
 
 # Dump the list into three integers
-min_reads = " ".join(min_reads)
+min_reads = " ".join([str(x) for x in min_reads])
 
 ref = snakemake.params.get("ref", None)
 if ref is None:

bio/gatk/variantrecalibrator/wrapper.py

@@ -35,19 +35,17 @@ def fmt_res(resname, resparams):
     "--resource {}".format(fmt_res(resname, resparams))
     for resname, resparams in snakemake.params["resources"].items()
 ]
+resources = " ".join(resources)
 annotation = " ".join(list(map("-an {}".format, snakemake.params.annotation)))
 tranches = ""
 if snakemake.output.tranches:
     tranches = "--tranches-file " + snakemake.output.tranches
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
-command = (
+os.system(
     f"gatk --java-options '{java_opts}' VariantRecalibrator {extra} {resources} "
     f"-R {snakemake.input.ref} -V {snakemake.input.vcf} "
     f"-mode {snakemake.params.mode} "
     f"--output {snakemake.output.vcf} "
     f"{tranches} {annotation} {log}"
 )
-print("COMMAND")
-print(command)
-os.system(command)

bio/multiqc/wrapper.py

@@ -10,7 +10,8 @@
 from os import path
 
 
-input_dirs = set(path.dirname(fp) for fp in snakemake.input)
+input_dirs = list(set(path.dirname(fp) for fp in snakemake.input))
+input_dirs = " ".join(input_dirs)
 output_dir = path.dirname(snakemake.output[0])
 output_name = path.basename(snakemake.output[0])
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)

bio/varscan/mpileup2indel/wrapper.py

@@ -24,15 +24,14 @@
 )
 
 # Building output directories
-os.makedirs(op.dirname(snakemake.output[0]))
+output_dir = op.dirname(snakemake.output[0])
+if not os.path.exists(output_dir):
+    os.makedirs(output_dir)
 
-command = (
+os.system(
     f'/bin/bash -c "varscan mpileup2indel '  # Tool and its subprocess
     f"{extra} "  # Extra parameters
     f"<( {pileup} ) "
     f"> {snakemake.output[0]} "  # Path to vcf file
     f'{log}"'  # Logging behaviour
 )
-
-print(command)
-os.system(command)

bio/varscan/mpileup2snp/wrapper.py

@@ -24,7 +24,9 @@
 )
 
 # Building output directories
-os.makedirs(op.dirname(snakemake.output[0]))
+output_dir = op.dirname(snakemake.output[0])
+if not os.path.exists(output_dir):
+    os.makedirs(output_dir)
 
 os.system(
     f'/bin/bash -c "varscan mpileup2snp '  # Tool and its subprocess