Pipeline fails on settings file without DEA when trying to collate deseq reports

[alexg9010]

This is the command that I used:

 $ export PIGX_UNINSTALLED="1" ; ./pigx-rnaseq -s tests/settings_no_de.yaml tests/sample_sheet.csv
 Job counts:
        count   jobs
        1       all
        1       collate_read_counts
        6       count_reads
        1       counts_from_SALMON
        6       coverage_megadepth
        1       deseq_collate_report1
        1       deseq_collate_report2
        1       deseq_collate_report3
        1       hisat2_index
        6       hisat2_map
        6       index_bam
        1       multiqc
        1       norm_counts_deseq
        1       salmon_index
        6       salmon_quant
        40

 [Thu Apr  4 11:42:51 2024]
Error in rule deseq_collate_report1:
    jobid: 39
    output: /fast/home/a/agosdsc/projects/pigx/pigx_rnaseq/tests/output/report/hisat2/collated.deseq_results.tsv
    log: /fast/home/a/agosdsc/projects/pigx/pigx_rnaseq/tests/output/logs/hisat2/collate_deseq.report.log (check log file(s) for error message)
    shell:
        /gnu/store/b0skxv953fpsdg79cs4g9qz78ds6pvlz-profile/bin/Rscript --vanilla /fast/home/a/agosdsc/projects/pigx/pigx_rnaseq/scripts/collate_deseq_results.R hisat2 /fast/home/a/agosdsc/projects/pigx/pigx_rnaseq/tests/output/report/hisat2 /fast/home/a/agosdsc/projects/pigx/pigx_rnaseq/tests/output/report/hisat2 >> /fast/home/a/agosdsc/projects/pigx/pigx_rnaseq/tests/output/logs/hisat2/collate_deseq.report.log 2>&1
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[....]

Content of /fast/home/a/agosdsc/projects/pigx/pigx_rnaseq/tests/output/logs/hisat2/collate_deseq.report.log:

Error in `colnames<-`(`*tmp*`, value = paste(rep(names(mylist), sapply(mylist,  :
  attempt to set 'colnames' on an object with less than two dimensions
Calls: multimerge -> colnames<-
Execution halted

I guess that collating should only happen when DEA's have been defined.

[borauyar]

@FrancescoSantini could you please have a look into this error and provide a fix for this issue?

[borauyar]

Fixed here https://github.com/BIMSBbioinfo/pigx_rnaseq/pull/143

[alexg9010]

Cool, thanks @FrancescoSantini !