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nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
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Channel mixup before `hostremoval_input_fastq` process #888

Closed maxibor closed 2 years ago

maxibor commented 2 years ago

Check Documentation

I have checked the following places for your error:

Description of the bug

It seems that channels get mixed up to the wrong elements in the map for the channel leading to the hostremoval_input_fastq: What should be a bam file ends up being a fastq file (R1)

Error executing process > 'hostremoval_input_fastq (JK2782)'

Caused by:
  Process `hostremoval_input_fastq (JK2782)` terminated with an error exit status (1)

Command executed:

  samtools index JK2782_R1_lanemerged.fq.gz
  extract_map_reads.py JK2782_R1_lanemerged.fq.gz JK2782_PE.mapped.bam -rev JK2782_PE.mapped.bam.bai -m remove -merged -of JK2782_R1_lanemerged.fq.hostremoved.fwd.fq.gz -or JK2782_R1_lanemerged.fq.hostremoved.rev.fq.gz -t 2

Command exit status:
  1

Command output:
  (empty)

Command error:
  samtools index: "JK2782_R1_lanemerged.fq.gz" is in a format that cannot be usefully indexed

This is probably coming from here: https://github.com/maxibor/eager/blob/889b7a0d9cab5f62eec2335811b53c605173f941/main.nf#L1488-1518

Steps to reproduce

Steps to reproduce the behaviour:

nextflow run maxibor/eager -r dev -profile eva,archgen,test_tsv_complex --hostremoval_input_fastq

Expected behaviour

$bam in the process should be a bam file.

jfy133 commented 2 years ago

I am unable to replicate neither on my local machine nor on the EVA cluster.

I note you are running from your own fork, maybe there is a change made ther somewhere?

i.e. this owrks fine for me with no error

nextflow run nf-core/eager -r dev -profile eva,archgen,test_tsv_complex --hostremoval_input_fastq