#!/usr/bin/env python

from anadama2 import Workflow
import os

workflow = Workflow(version="0.0.2",
    description="A workflow to run PanPhlAn")

workflow.add_argument("threads", default=1,
    desc="number of threads for panphlan to use")
workflow.add_argument("dbfolder", default=None,
    desc="folder containing database")
workflow.add_argument("filesfile", default=None,
    desc="file with filepaths to run on (relative to input)")
workflow.add_argument("ref", default="prevotella",
    desc="name of reference db")
workflow.add_argument("refs", default=None,
    desc="file with list of references (relative to dbfolder)")


args = workflow.parse_args()

in_files = workflow.get_input_files(".fastq.gz")
out_files = workflow.name_output_files(name=in_files, tag="panphlan_map", extension="csv.bz2")

if args.filesfile:
    with open(args.filesfile) as f:
        in_files = [l.strip() for l in f]

if args.dbfolder:
    cmd = "panphlan_map.py -c [reference] -i [depend] -o [target] -p [threads] --i_bowtie2_indexes [db]"
else:
    cmd = "panphlan_map.py -c [reference] -i [depend] -o [target] -p [threads]"

skipped = open("{}/{}/skippedfiles.txt".format(args.output, ref), "w")

if args.ref
    refs = [args.ref]
elif args.refs
    r = open(args.refs, "r")
    refs = readlines(r)
    r.close()


for f in in_files:
    if not os.path.isdir("{}/{}".format(args.output, ref)):
        os.makedirs("{}/{}".format(args.output, ref))
    fq_path = os.path.join(args.input, f)

    if args.filesfile:
        if not fq_path in files:
            skipped.write("{}\n".format(f))
    elif not os.path.isfile(fq_path):
        continue

    for ref in refs
        workflow.add_task_gridable(
            cmd, reference=ref,
            depend=fq_path,
            target="{}/{}/{}_panphlan_map.csv.bz".format(args.output, ref, f.strip(".fastq.gz")),
            folder=args.output,
            threads=args.threads,
            cores=args.threads,
            db=args.dbfolder,
            time=4*60, mem=8*1000)

skipped.close()

workflow.go()

@@ -1193,16 +1193,17 @@
 args.ref
+:
 %0A    ref
@@ -1227,24 +1227,25 @@
 if args.refs
+:
 %0A    r = ope

fix syntax