Commit dc54ef14 authored by alex's avatar alex

add wide-band flagging step

parent 0abf7d39
Pipeline #10295 failed with stages
in 2 minutes and 12 seconds
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.0
id: aoflagger
hints:
DockerRequirement:
dockerPull: lofareosc/prefactor:HBAcalibrator
baseCommand:
# - aoflagger
- /bin/bash
- script.sh
inputs:
- id: msin
type: Directory[]
doc: Input measurement set
- id: concat_meta_ms
type: Directory
doc: Input measurement set
# inputBinding:
# position: 0
- id: concat_additional_ms
type: Directory
doc: Input measurement set
- id: verbose
type: boolean?
doc: will produce verbose output
inputBinding:
valueFrom: -v
- id: n_threads
type: int?
doc: |
overrides the number of threads specified in the strategy
(default: one thread for each CPU core)
inputBinding:
prefix: -j
- id: strategy
type: File?
doc: |
specifies a customized strategy
inputBinding:
prefix: -strategy
#### READ MODES
- id: direct_read
type: boolean?
doc: |
Will perform the slowest IO but will always work.
inputBinding:
prefix: -direct-read
- id: indirect_read
type: boolean?
doc: |
Will reorder the measurement set before starting, which is normally
faster but requires free disk space to reorder the data to.
inputBinding:
prefix: -indirect-read
- id: memory_read
type: boolean?
doc: |
Will read the entire measurement set in memory. This is the fastest,
but requires much memory.
inputBinding:
prefix: -memory-read
- id: auto_read
type: boolean?
doc: |
Will select either memory or direct mode based on available memory (default).
inputBinding:
prefix: -auto-read
##############
- id: skip_flagged
type: boolean?
doc: |
Will skip an ms if it has already been processed by AOFlagger according
to its HISTORY table.
inputBinding:
prefix: -skip-flagged
- id: uvw
type: File?
doc: Reads uvw values (some exotic strategies require these)
inputBinding:
prefix: -uvw
- id: column
type: string?
doc: Specify column to flag
inputBinding:
prefix: -column
- id: bands
type: int[]?
doc: Comma separated list of (zero-indexed) band ids to process
inputBinding:
prefix: -bands
itemSeparator: ','
- id: fields
type: int[]?
doc: Comma separated list of (zero-indexed) field ids to process
inputBinding:
prefix: -fields
itemSeparator: ','
- id: combine-spws
type: boolean?
doc: Join all SPWs together in frequency direction before flagging
inputBinding:
prefix: -combine-spws
- id: bandpass
type: File?
doc: Set bandpass correction file for any 'Apply passband' action
inputBinding:
prefix: bandpass
outputs:
- id: output_ms
doc: Output MS
type: Directory[]
outputBinding:
glob: 'workdir/out_*'
- id: logfile
type: File?
outputBinding:
glob: aoflag.log
label: AOFlagger
requirements:
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.msin)
writable: true
- entry: $(inputs.concat_meta_ms)
writable: true
- entry: $(inputs.concat_additional_ms)
writable: true
- entryname: script.sh
entry: |
#!/bin/bash
directories=\$(ls -d out*)
echo \$directories
mkdir -pv workdir
cp -r \$directories workdir/. && cd workdir
concat=out.MS_[0-9*]
echo \$1 \$2 \$3 \$4 \$concat
aoflagger \$1 \$2 \$3 \$4 \$concat
stdout: aoflag.log
stderr: aoflag_err.log
\ No newline at end of file
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