Open drothen15 opened 5 months ago
I created the bismark index and kept the reference file within the folder ( not soft link), then re-ran it using --bismark_index and that seems to solve it for now.
should have been fixed by #403
I created the bismark index and kept the reference file within the folder ( not soft link), then re-ran it using --bismark_index and that seems to solve it for now.
Hi,
I am having the same issue and am not sure that #403 fixed it. What do you mean with adding the bismark index, do you provide the path to the bismark index after --bismark_index or do you have to place the index somewhere specific?
thanks in advance for your help!
I have the exact same issue and when going through the codes, I notice the following scripts in the local module "prepare_genome.nf",
// Aligner: bwameth
else if ( params.aligner == 'bwameth' ){
/*
* Generate bwameth index if not supplied
*/
if (params.bwa_meth_index) {
if (params.bwa_meth_index.endsWith('.tar.gz')) {
ch_bismark_index = UNTAR ( [ [:], file(params.bwa_meth_index) ] ).untar.map { it[1] }
} else {
ch_bismark_index = Channel.value(file(params.bwa_meth_index))
}
} else {
BWAMETH_INDEX(ch_fasta)
ch_bwameth_index = BWAMETH_INDEX.out.index
ch_versions = ch_versions.mix(BWAMETH_INDEX.out.versions)
}
When providing bwameth index, either compressed or uncompressed format, it will pass to ch_bismark_index
, while if providing only the fasta for indexing by the module BWAMETH_INDEX
, it will pass to ch_bwameth_index
.
I suppose ch_bismark_index
here should be ch_bwameth_index
, and this probably explains why using iGenome fasta or providing --bismark_index
make the pipeline works.
I changed all ch_bismark_index
to ch_bwameth_index
and it works well now.
Description of the bug
I have previously processed the GRCh38 genome with bwameth for a different pipeline that I'm trying to compare with the nf-core. So I provide the following with the input command: --fasta --fasta_index --bwa_meth_index
However, everytime I do this the pipeline just skips all the bwameth steps in the pipeline and then completes without error (screenshot).
Command used and terminal output
Relevant files
nextflow.log
System information
Nextflow version: 23.10.1 Hardware: HPC Executor: slurm Container engine: apptainer OS: Linux MethylSeq version: 2.6.0