This doesn’t appear to solve the issue. When I run this, neither --transcript-pkl nor --spots-pkl get passed to the python script, as was the problem with the original specification.
Is this because of the older cwltool version?
Output from the original cwl file is as follows:
INFO /home/ubuntu/miniconda3/bin/cwltool 3.0.20200807132242
INFO Resolved 'steps/qc.cwl' to 'file:///mnt/cwl/spatial-transcriptomics-pipeline/steps/qc.cwl'
INFO [job qc.cwl] /mnt/tmp/q79zrf03$ docker \
run \
-i \
--mount=type=bind,source=/mnt/tmp/q79zrf03,target=/QqJZyL \
--mount=type=bind,source=/mnt/tmp/twe21v3l,target=/tmp \
--mount=type=bind,source=/mnt/data/intron_rep4/txprocconverted,target=/var/lib/cwl/stg30946621-981e-433e-9a12-f6dc94732882/txprocconverted,readonly \
--mount=type=bind,source=/mnt/data/intron_rep4/collab_segmask/RoiSet.zip,target=/var/lib/cwl/stgcb9d5cff-e696-432c-9f62-77ac9ded27eb/RoiSet.zip,readonly \
--workdir=/QqJZyL \
--read-only=true \
--net=none \
--user=1000:1000 \
--rm \
--env=TMPDIR=/tmp \
--env=HOME=/QqJZyL \
--cidfile=/mnt/tmp/7x2zhu9g/20210913200455-524223.cid \
docker.pkg.github.com/hubmapconsortium/spatial-transcriptomics-pipeline/starfish:latest \
/opt/qcDriver.py \
--codebook-exp \
/var/lib/cwl/stg30946621-981e-433e-9a12-f6dc94732882/txprocconverted \
--roi \
/var/lib/cwl/stgcb9d5cff-e696-432c-9f62-77ac9ded27eb/RoiSet.zip \
--x-size \
2048 \
--y-size \
2048 \
--z-size \
11
Namespace(codebook_exp=PosixPath('/var/lib/cwl/stg30946621-981e-433e-9a12-f6dc94732882/txprocconverted'), codebook_pkl=None, roi=PosixPath('/var/lib/cwl/stgcb9d5cff-e696-432c-9f62-77ac9ded27eb/RoiSet.zip'), run_ripley=False, spots_exp=None, spots_pkl=None, transcript_exp=None, transcript_pkl=None, x_size=2048, y_size=2048, z_size=11)
100%|██████████| 1740/1740 [00:49<00:00, 35.24it/s]
Traceback (most recent call last):
File "/opt/qcDriver.py", line 527, in <module>
run("6_qc/", transcripts, codebook, size, spots, roi, args.run_ripley)
File "/opt/qcDriver.py", line 462, in run
trRes["density"] = getTranscriptDensity(transcripts, codebook)
File "/opt/qcDriver.py", line 342, in getTranscriptDensity
return np.shape(transcripts.data)[0] / len(codebook.target)
AttributeError: 'bool' object has no attribute 'data'
INFO [job qc.cwl] Max memory used: 0MiB
WARNING [job qc.cwl] completed permanentFail
{
"qc_metrics": {
"location": "file:///mnt/cwl/spatial-transcriptomics-pipeline/6_qc",
"basename": "6_qc",
"class": "Directory",
"listing": [
{
"class": "File",
"location": "file:///mnt/cwl/spatial-transcriptomics-pipeline/6_qc/2021-13-09_20%3A07_TXconversion.log",
"basename": "2021-13-09_20:07_TXconversion.log",
"checksum": "sha1$f31d422fcd03428b6453affd6d33771d4b7ca133",
"size": 1312,
"path": "/mnt/cwl/spatial-transcriptomics-pipeline/6_qc/2021-13-09_20:07_TXconversion.log"
},
{
"class": "File",
"location": "file:///mnt/cwl/spatial-transcriptomics-pipeline/6_qc/graph_output.pdf",
"basename": "graph_output.pdf",
"checksum": "sha1$27cdda449b113741c48f2bfc05ce7332e72bc655",
"size": 208,
"path": "/mnt/cwl/spatial-transcriptomics-pipeline/6_qc/graph_output.pdf"
}
],
"path": "/mnt/cwl/spatial-transcriptomics-pipeline/6_qc"
}
}
WARNING Final process status is permanentFail