failing to run rnaseq-nf pipeline with "Is a directory" error

[kulesha]

must be something in my setup as nobody else seems to have reported the issue
any advice how to tackle that ?

$> nextflow run rnaseq-nf
N E X T F L O W  ~  version 22.04.0
Launching `https://github.com/nextflow-io/rnaseq-nf` [stoic_meninsky] DSL2 - revision: ed179ef74d [master]
 R N A S E Q - N F   P I P E L I N E
 ===================================
 transcriptome: /tmp/analysis/0/nextflow-io/rnaseq-nf/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
 reads        : /tmp/analysis/0/nextflow-io/rnaseq-nf/data/ggal/ggal_gut_{1,2}.fq
 outdir       : results

Is a directory

 -- Check script 'nextflow-io/rnaseq-nf/./modules/rnaseq.nf' at line: 3 or see '.nextflow.log' file for more details
$>

in .nextflow.log I see

Feb-22 14:25:24.522 [main] DEBUG nextflow.Session - Session aborted -- Cause: Is a directory
Feb-22 14:25:24.536 [main] ERROR nextflow.cli.Launcher - Is a directory
java.io.IOException: Is a directory

[pditommaso]

Can you please properly format the question to make it readable?

[pditommaso]

can you include the full error stack trace please? also I've advice to update to latest version 22.10.7

[kulesha]

it looks like upgrading to v22.10.7 fixed the directory issue

>/tmp/analysis/10$ nextflow run rnaseq-nf
N E X T F L O W  ~  version 22.10.7
Pulling nextflow-io/rnaseq-nf ...
 downloaded from https://github.com/nextflow-io/rnaseq-nf.git
Launching `https://github.com/nextflow-io/rnaseq-nf` [voluminous_ride] DSL2 - revision: ed179ef74d [master]
 R N A S E Q - N F   P I P E L I N E
 ===================================
 transcriptome: /tmp/analysis/10/nextflow-io/rnaseq-nf/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
 reads        : /tmp/analysis/10/nextflow-io/rnaseq-nf/data/ggal/ggal_gut_{1,2}.fq
 outdir       : results

executor >  local (2)
executor >  local (2)
[05/f5d96d] process > RNASEQ:INDEX (ggal_1_48850000_49020000) [100%] 1 of 1, failed: 1 ✘
[d0/f801cb] process > RNASEQ:FASTQC (FASTQC on ggal_gut)      [100%] 1 of 1, failed: 1 ✘
[-        ] process > RNASEQ:QUANT                            -
[-        ] process > MULTIQC                                 -
Error executing process > 'RNASEQ:INDEX (ggal_1_48850000_49020000)'

Caused by:
  Process `RNASEQ:INDEX (ggal_1_48850000_49020000)` terminated with an error exit status (127)

Command executed:

  salmon index --threads 1 -t ggal_1_48850000_49020000.Ggal71.500bpflank.fa -i index

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: salmon: command not found

Work dir:
  /tmp/analysis/10/work/05/f5d96d227b511d81095fc2d9fee517

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`



>/tmp/analysis/10$```

[kulesha]

and as i switched to use awsbatch executor it all fell into places )

executor >  awsbatch (4)
[bf/a9bd4b] process > RNASEQ:INDEX (ggal_1_48850000_49020000) [100%] 1 of 1 ✔
[0e/22ffbf] process > RNASEQ:FASTQC (FASTQC on ggal_gut)      [100%] 1 of 1 ✔
[0a/999613] process > RNASEQ:QUANT (ggal_gut)                 [100%] 1 of 1 ✔
[6d/3b5745] process > MULTIQC                                 [100%] 1 of 1 ✔

Done! Open the following report in your browser --> results/multiqc_report.html

Completed at: 22-Feb-2023 18:15:36
Duration    : 1m 41s
CPU hours   : (a few seconds)
Succeeded   : 4

thanks for your help !