Resume not working from modules where markersheet is collected #80
Description
Description of the bug
For modules where the marker sheet is collected to a file prior to execution, resume does not work.
Applies to Backsub and MCQUANT.
ch_mcquant_markers = ch_markersheet
.flatMap{
['marker_name'] +
it.collect{ _1, _2, marker_name, _4, _5, _6, _7, _8, _9 -> '"' + marker_name + '"' }
}
.dump(tag: "MARKERS")
.collectFile(name: 'markers.csv', sort: false, newLine: true)
Command used and terminal output
Backsub issue (notice lack of 'cached'):
nextflow run nf_mcmicro -profile test,docker --outdir ./tmp -resume --marker_sheet ./nf_mcmicro/assets/markers-test_backsub.csv --backsub
executor > local (4)
[17/5d07cb] NFCORE_MCMICRO:MCMICRO:ASHLAR (TEST1) | 1 of 1, cached: 1 ✔
[e2/65270b] NFCORE_MCMICRO:MCMICRO:BACKSUB (TEST1) | 1 of 1 ✔
[15/041dfc] NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER (TEST1) | 1 of 1 ✔
[- ] NFCORE_MCMICRO:MCMICRO:CELLPOSE -
[7c/b87c54] NFCORE_MCMICRO:MCMICRO:MCQUANT (TEST1) | 1 of 1 ✔
[7a/a1502f] NFCORE_MCMICRO:MCMICRO:MULTIQC | 1 of 1 ✔
-[nf-core/mcmicro] Pipeline completed successfully-
MCQUANT issue:
nextflow run nf_mcmicro -profile test,docker --outdir ./tmp -resume --marker_sheet ./nf_mcmicro/assets/markers-test.csv
executor > local (2)
[17/5d07cb] NFCORE_MCMICRO:MCMICRO:ASHLAR (TEST1) | 1 of 1, cached: 1 ✔
[22/e1725b] NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER (TEST1) | 1 of 1, cached: 1 ✔
[- ] NFCORE_MCMICRO:MCMICRO:CELLPOSE -
[1b/0bd06b] NFCORE_MCMICRO:MCMICRO:MCQUANT (TEST1) | 1 of 1 ✔
[bf/c83787] NFCORE_MCMICRO:MCMICRO:MULTIQC | 1 of 1 ✔
-[nf-core/mcmicro] Pipeline completed successfully-Relevant files
No response
System information
No response