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Published
20 hours ago •
thasso
thasso
Wrong Output --dry
Command:
jip run --dry MethRep.jip -i test_files/all.mult_diff.map -r test_files/rmsk.clean.bed -b TEST
#######################################################################################
| Pipeline Configuration |
+--------------------------------+----------------------------------------------------+
| Name | Value |
+================================+====================================================+
| input | test_files/all.mult_diff.map |
| repBed | test_files/rmsk.clean.bed |
| base | TEST |
| p | False |
+--------------------------------+----------------------------------------------------+
#######################################################################################
| Job - FilterMapping |
+--------------------------------+----------------------------------------------------+
| Name | Value |
+================================+====================================================+
| input | test_files/all.mult_diff.map |
| base | TEST |
| p | False |
| unique | TEST.unique.map |
| multi | TEST.mult.map |
| uniqOEA | TEST.uniq_OEA.map |
| multOEA | TEST.mult_OEA.map |
| multD | TEST.mult_diff.map |
+--------------------------------+----------------------------------------------------+
#######################################################################################
| Job - TEST |
+--------------------------------+----------------------------------------------------+
| Name | Value |
+================================+====================================================+
| input | [u'TEST.mult.map', u'TEST.unique.map', |
| | u'TEST.mult_OEA.map'] |
| cmd | [u'echo TEST.unique.map'] |
| outfile | |
| output | <<STREAM>> |
+--------------------------------+----------------------------------------------------+
#######################################################################################
| Job - TEST.1 |
+--------------------------------+----------------------------------------------------+
| Name | Value |
+================================+====================================================+
| input | [u'TEST.mult.map', u'TEST.unique.map', |
| | u'TEST.mult_OEA.map'] |
| cmd | [u'echo TEST.mult.map'] |
| outfile | |
| output | <<STREAM>> |
+--------------------------------+----------------------------------------------------+
#######################################################################################
| Job - TEST.2 |
+--------------------------------+----------------------------------------------------+
| Name | Value |
+================================+====================================================+
| input | [u'TEST.mult.map', u'TEST.unique.map', |
| | u'TEST.mult_OEA.map'] |
| cmd | [u'echo TEST.mult_OEA.map'] |
| outfile | |
| output | <<STREAM>> |
+--------------------------------+----------------------------------------------------+
#####################################################################################################################################################
| Job states |
+--------------------------------+--------+----------------------------------------------------+----------------------------------------------------+
| Name | State | Inputs | Outputs |
+================================+========+====================================================+====================================================+
| FilterMapping | Hold | test_files/all.mult_diff.map | TEST.unique.map, TEST.mult.map, TEST.uniq_OEA.map, |
| | | | TEST.mult_OEA.map, TEST.mult_diff.map |
| TEST | Hold | TEST.mult.map, TEST.unique.map, TEST.mult_OEA.map | |
| TEST.1 | Hold | TEST.mult.map, TEST.unique.map, TEST.mult_OEA.map | |
| TEST.2 | Hold | TEST.mult.map, TEST.unique.map, TEST.mult_OEA.map | |
+--------------------------------+--------+----------------------------------------------------+----------------------------------------------------+
#####################
| Job hierarchy |
#####################
FilterMapping (MethRep)
├─TEST
├─TEST.1
└─TEST.2
#####################
| Tasks: 4 |
| Jobs: 4 |
| Named Groups: 1 |
| Job Groups: 1 |
#####################
Files used:
FilterMap.jip:
#!/usr/bin/env jip
# Split map files by their mappings
#
# Usage:
# FilterMap.jip -i <MapFile> [-b <prefix_output>] [-p]
#
# Inputs:
# -i, --input <MapFilet> MAP file
#
# Options:
# -b, --base <prefix_output> Prefix name output [default: out]
# -p Data is paired-end
#
#
#
#%begin init
add_output('unique', '${base}.unique.map')
add_output('multi', '${base}.mult.map')
add_output('uniqOEA', '${base}.uniq_OEA.map')
add_output('multOEA', '${base}.mult_OEA.map')
add_output('multD', '${base}.mult_diff.map')
#%end
echo "${input}"
python filter_map.py -i ${input} -o ${base} ${p|arg("-p")}
MethRep.jip: #! /usr/bin/env jip # #Locate reads that map in repetitive regions # #Usage: # MetRep.jip -i -r <rmsk.bed> -b <prefix_output> [-p] # #Inputs: # -i, --input Mapping file from gem # -r, --repBed <rmsk.bed> Repetitive regions in BED format # # #Options: # -b, --base <prefix_output> Prefix output # -p Flag if mapping is paired #
#%begin pipeline
sepMap = job('FilterMapping').run("FilterMap", input=opts["input"], base=base, p=p)
f = job("${base}").bash("echo ${input}", input=[sepMap.unique, sepMap.multi, sepMap.multOEA])
#%end
