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Hello, I’m running 2.1.0 for the first time and I’...
# chipseq
s
Hello, I’m running 2.1.0 for the first time and I’m getting the following error: `Process 
NFCORE_CHIPSEQ:PREPARE_GENOME:GFFREAD
declares 2 input channels but 1 were specified` . Here’s my submission code and the .log file is attached. Any help would be greatly appreciated!
Copy code
nextflow run $PIPES/nfcore_chipseq/nf-core-chipseq_2.1.0/2_1_0 \
  --input $PROJECT/data/sample_sheets/sample_sheet.csv \
  --outdir $PROJECT/results \
  --fasta $GENOME/arabidopsis_thaliana/ensembl_release60/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa \
  --gff $GENOME/arabidopsis_thaliana/ensembl_release60/Arabidopsis_thaliana.TAIR10.60.gff \
  --blacklist $GENOME/arabidopsis_thaliana/ensembl_release60/TAIR10.Klasfeld.arabidopsis_greenscreen_20inputs_MtPt.bed \
  --narrow_peak \
  --read_length 150 \
  -profile singularity \
  -c $PIPES/nfcore_chipseq/src/slurm.config.sh \
  -w $SCRATCH/thomashowm/BCC117_chipseq
nextflow.log
👍 1
f
Hello everybody, today I stumbled upon the same issue. It seems that the 
<http://prepare_genome.nf|prepare_genome.nf>
subworkflow has a little bug in line 75. The `GFFREAD` module expects two channels as input but only the first one is provided - the tuple. I tried to add the 
ch_fasta
channel as second input but that generates another error which may be linked to how I am running Nextflow (
-profile singularity
)
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Nov-15 18:22:08.713 [Actor Thread 4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_CHIPSEQ:PREPARE_GENOME:GFFREAD; work-dir=null
  error [nextflow.exception.ProcessUnrecoverableException]: Not a valid path value type: groovyx.gpars.dataflow.DataflowVariable (DataflowVariable(value=/home/francesco/Projects/chipseq/my-test/genes.gff)
I tried multiple profiles (singularity, apptainer and conda) but I always get the same error. The file is in the correct place (
/home/francesco/Projects/chipseq/my-test/genes.gff
).
Hello, I managed to solve the issue for non-gzipped gff files. I haven't opened a PR yet because I would like to fix the gzipped branch as well. https://github.com/ftabaro/nf-core-chipseq/blob/cb1317e0b4fe77be3e7823a862bc50418584e37d/subworkflows/local/prepare_genome.nf#L73 Working on it, I noticed that GFFREAD outputs 
null.gtf
. In the module, the process expects 
ext.prefix
, which is not set in 
config/modules.conf
or 
meta.id
from the input channel. The pipeline still works but the gtf has that weird name. Shall we fix it somehow? Should we explicit 
ext.prefix
in 
modules.config
to something fixed (e.g. 
genes
), or should we implement some logic to get the actual name from the input gff? On my dev machine I am trying the latter and plan to commit later today. There is also another issue with the map on line 75 which was already addressed 🙂
j
Hi @Francesco Tabaro, I saw your PR yesterday Thanks! I will try to review it today 😃
👍 1
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