I am trying to set up nf-chipseq for a large project. we have thousands of chipseq data sets on hundreds of genomes of small eukaryotic parasites, so not in iGenomes. I have no trouble running the Test workflow, but I get this error from GFFREAD when I try to run my own workflow with --fasta and --gff paramemters. It seems the GFFREAD in prepare_genome.nf is not getting the fasta file from the --fasta CLI parameter. I can see the fasta and gff in the NF core intro message (but it refuses to find custom config files). N E X T F L O W ~ version 24.10.3 Launching

<https://github.com/nf-core/chipseq>

[sad_roentgen] DSL2 - revision: 76e2382b6d [master] ------------------------------------------------------ ,--./,-. _ _ _ __ _ /,-._.--~' |\ | |__ _ / ` / \ |_) |__ } { | \| | \__, \__/ | \ |___ \`-._,-

-,

.,.,' nf-core/chipseq v2.1.0-g76e2382 ------------------------------------------------------ Core Nextflow options revision : master runName : sad_roentgen containerEngine: docker launchDir : /Users/browns02-adm/ChipSeq workDir : /Users/browns02-adm/ChipSeq/work projectDir : /Users/browns02-adm/.nextflow/assets/nf-core/chipseq userName : browns02-adm profile : docker configFiles : Input/output options input : samplesheet.csv read_length : 150 outdir : Data Reference genome options fasta : RefGenomes/ToxoDB-68_TgondiiME49_Genome.fasta gff : RefGenomes/ToxoDB-68_TgondiiME49.gff macs_gsize : 80000000 Alignment options aligner : bowtie2 my command line:

% nextflow run nf-core/chipseq --fasta RefGenomes/ToxoDB-68_TgondiiME49_Genome.fasta --gff RefGenomes/ToxoDB-68_TgondiiME49.gff --outdir Data --input samplesheet.csv -profile docker --aligner bowtie2 --read_length 150 --macs_gsize 80000000

my error message:

Process NFCORE_CHIPSEQ:PREPARE_GENOME:GFFREAD declares 2 input channels but 1 were specified

 -- Check script '/Users/browns02-adm/.nextflow/assets/nf-core/chipseq/./subworkflows/local/prepare_genome.nf' at line: 75 or see '.nextflow.log' file for more details

I tried to add a custom config file that contains the "-g" parameter for GFFREAD, but this is ignored and I get the same error. I also tried single quotes around the path to custom config file (as stated here https://github.com/nf-core/configs) and this is also ignored. my custom config file:

process {
  withName: GFFREAD {
    ext.args = "-g RefGenomes/ToxoDB-68_TgondiiME49_Genome.fasta"
  }
}

my command line with -c param

% nextflow run nf-core/chipseq --fasta RefGenomes/ToxoDB-68_TgondiiME49_Genome.fasta --gff RefGenomes/ToxoDB-68_TgondiiME49.gff --outdir Data --input samplesheet.csv -profile docker --aligner bowtie2 --read_length 150 --macs_gsize 80000000 -c 'chip.config'

this seems to have been fixed in the current dev version (see PR #435). hope it works if you re-run with

-r dev

I ran with the -r dev. It now gives a somewhat different error from GFFREAD. Here is my command line and the error:

% nextflow run nf-core/chipseq --fasta RefGenomes/ToxoDB-68_TgondiiME49_Genome.fasta --gff RefGenomes/ToxoDB-68_TgondiiME49.gff --outdir Data --input samplesheet.csv -profile docker --aligner bowtie2 --read_length 150 --macs_gsize 80000000 -c '/Users/browns02-adm/ChipSeq/chip.config' -r dev

 N E X T F L O W  ~ version 24.10.3

Launching `<https://github.com/nf-core/chipseq>` [disturbed_nobel] DSL2 - revision: 73a5304872 [dev]

Downloading plugin nf-schema@2.1.1

------------------------------------------------------
                    ,--./,-.
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 |\ | |__ __ / ` / \ |__) |__     } {
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                    `._,._,'
 nf-core/chipseq 2.2.0dev
.
.
userName    : browns02-adm
 profile    : docker
 configFiles  :

[-    ] NFCORE_CHIPSEQ:CHIPSEQ:IGV                                 [ 0%] 0 of 1
Plus 33 more processes waiting for tasks…
Execution cancelled -- 
-[nf-core/chipseq] Pipeline completed with errors-
WARN: Input tuple does not match tuple declaration in process `NFCORE_CHIPSEQ:PREPARE_GENOME:GFFREAD` -- offending value: /Users/browns02-adm/ChipSeq/RefGenomes/ToxoDB-68_TgondiiME49.gff
ERROR ~ Execution aborted due to an unexpected error

 -- Check script '/Users/browns02-adm/.nextflow/assets/nf-core/chipseq/./subworkflows/local/../../modules/nf-core/gffread/main.nf' at line: 6 or see '.nextflow.log' file for more details

I am not sure, have you investigated the corresponding prcess directory under

work/

. You could try to run the commands (check contents of

.command.sh

) there independently and see if they actually work in case there is an issue with the gff file or corrupted files from previous runs.

Hi, this was actually an issue when the

gff

file is provided by the user because when we were creating the corresponding we did not add an empty map to it, this PR should fix the issue in

dev

once merged. Maybe you can give at 👀 and accept it, otherwise you can try to run the pipeline from my branch (it is exactly as dev but with the fix) BTW, it is not good practise to pass files on a custom config since if they are not passed to the process by a channel they won’t be there, actually this is what it happens on this case as the file it is not staged by the

GFFREAD

process but anyway it should work without the fasta