Proposal: Rewrite SRA_RUNINFO_TO_FTP as native process #36
GitHub Actions / JUnit Test Report
failed
Feb 21, 2025 in 0s
1 tests run, 0 passed, 0 skipped, 1 failed.
Annotations
Check failure on line 1 in Test process: SRA_RUNINFO_TO_FTP
github-actions / JUnit Test Report
Test process: SRA_RUNINFO_TO_FTP.Should run without failures
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 25.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/.nf-test-6bf37c565f01081614eef23b595d02a8.nf` [curious_faraday] DSL2 - revision: 06b19695f4
Downloading plugin [email protected]
Downloading plugin [email protected]
[36/491ce6] Submitted process > SRA_RUNINFO_TO_FTP
ERROR ~ Error executing process > 'SRA_RUNINFO_TO_FTP'
Caused by:
No such file or directory: SRR13191702.runinfo.tsv
Source block:
def (runinfo, header) = parseSraRuninfo(runinfo_file)
header.add(0, "id")
def samplesheet = [:]
runinfo.each { db_id, rows ->
if( db_id !in samplesheet )
samplesheet[db_id] = rows
else
log.warn("Duplicate sample identifier found -- ID: '${db_id}'")
}
def prefix = runinfo_file.name.tokenize(".")[0]
def file_out = task.workDir.resolve("${prefix}.runinfo_ftp.tsv")
file_out << header.join("\t") << "\n"
samplesheet
.sort { id, _rows -> id }
.each { id, rows ->
rows.each { row ->
row.id = row.run_accession
? "${id}_${row.run_accession}"
: id
def values = header.collect { k -> row[k] }
file_out << values.join("\t") << "\n"
}
}
Work dir:
/home/runner/work/fetchngs/fetchngs/~/tests/6bf37c565f01081614eef23b595d02a8/work/36/491ce63f9c67c52c20a22f6fa40747
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '/home/runner/work/fetchngs/fetchngs/~/tests/6bf37c565f01081614eef23b595d02a8/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:
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