Closed spraeger closed 5 months ago
Hey @spraeger
Thanks for reporting your issue. The error arises because the channel which contains the groups parameter is out of sync with the channels which feed the dpsi and psivec parameters. This occurs because Nextflow processes are not guaranteed to return results in the order they arrive from the input channel. This is easily overlooked, and I can only apologise. I've prototyped a solution and will try and get it posted tomorrow as a hot fix for you to test with your data.
James
Hello @spraeger,
I've submitted a pull request with the proposed fix. Could you please test it and let me know if it resolves the issue for you? I'll need to hold off on merging and releasing it until it undergoes a second code review. Thanks!
Hi @jma1991,
Thanks a lot for clarification and the prompt action! I have tested your patch and it resolves the issue for my data.
Hey @spraeger
We have just released 1.0.4 which has this issued fixed. Thanks for bringing it to our attention.
Description of the bug
Hi, For one of my contrasts (pdx_41-control_don) the group parameter for CLUSTEREVENTS_IOI (suppa_clusterevents.nf) is assigned incorrectly, so that
ERROR:lib.cluster_tools:Invalid index. Index 6 is smaller than the number of columns in the file (7).
occurs. For all other contrasts, the clustergroup assignment works fine.The related pdx_41-control_don_transcript_diffsplice.psivec file contains seven columns, the correct grouping would be
--groups 1-4,5-7
:It seems that the derivation of the clustergroups for this contrast was never started. The related work directory 0d/4f97644516640eda4e35d88e4dab59 is empty.
However, CLUSTEREVENTS_IOI is executed with
--groups 1-3,4-6
which causes the error to occur. Could you please help me to understand why and at which point the assignment--groups 1-3,4-6
is made, as CLUSTERGROUPS does not seem to run? Thank you in advance!Command used and terminal output
Relevant files
contrastsheet_pdx_group.csv samplesheet_pdx_group.csv
System information
CentOS Linux release 7.9.2009 (Core), LSF Cluster Nextflow version 23.10.1 $(RNASPLICE_DIR) in the pipeline call refers to a fork of nf-core/rnasplice v1.0.2 that increases alignment resources (https://github.com/dkoppstein/rnasplice/tree/increase_sam)