Open s-andrews opened 3 years ago
Hmm, commas in filenames... what can possibly go wrong? Which downloading tool would ever allow this....
I can confirm that it is the comma in the filename that breaks it, replacing it with _
works just fine. So, is this a case of stop wanting to submit files with commas
, or does the Nextflow pipeline have to sort this out?
To be fair a comma is a pretty unfriendly thing to put in a file name, but it's not a disallowed character so we should probably deal with it.
The names came from sradownloader so I'll have a look at what was going on with that too.
A fix from both ends would seem to be the appropriate fix :-)
OK, if you want to upgrade this to a proper bug then it still fails even with --single_end
as a parameter. Trim galore still gets run in paried end mode.
The command used to launch the workflow was as follows:
nextflow /bi/apps/nextflow/nextflow_pipelines/nf_chipseq --genome GRCm38 -bg --single_end SRR1917137_GSM1635411_Ikaros_ChIP-Seq,_proB_cells_Mus_musculus_ChIP-Seq_1.fastq.gz SRR1917139_GSM1635413_Brg1_ChIP-Seq,_proB_cells_Mus_musculus_ChIP-Seq_1.fastq.gz SRR1917140_GSM1635414_Input,_proB_cells_Mus_musculus_ChIP-Seq_1.fastq.gz
Execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 255.
The full error message was:
Error executing process > 'TRIM_GALORE (null)'
Caused by:
Process `TRIM_GALORE (null)` terminated with an error exit status (255)
Command executed:
module load trim_galore
module load fastqc
trim_galore --paired SRR1917139_GSM1635413_Brg1_ChIP-Seq,_proB_cells_Mus_musculus_ChIP-Seq_1.fastq.gz SRR1917140_GSM1635414_Input,_proB_cells_Mus_musculus_ChIP-Seq_1.fastq.gz
With file names:
The pipeline somehow decided that these are paired.