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NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.
https://www.earthbiogenome.org/
GNU General Public License v3.0
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Hifiasm missing p_ctgs in output. #65

Closed gbdias closed 7 months ago

gbdias commented 7 months ago

Describe the bug Hifiasm process does not output *asm.p_ctgs.fa. Only hap1 and hap2 are produced.

To Reproduce Steps to reproduce the behavior: Ran the pipeline (version 2b8526aa3b2d86fc6ea57c0b86d4e3b1b3c3264f) with PacBio HiFi data only.

#! /usr/bin/env bash
#SBATCH -A naiss2023-5-307
#SBATCH -p core
#SBATCH -n 1
#SBATCH -t 1-00:00:00
#SBATCH -J gc_ebp

RESULTS="${PWD/analyses/data/outputs}"
NEXTFLOW_OPTS=${NEXTFLOW_OPTS:-"-resume -ansi-log false"}
export NXF_SINGULARITY_CACHEDIR=${NXF_SINGULARITY_CACHEDIR:-"/proj/snic2021-6-194/nobackup/ebp-singularity-cache"}

source activate nextflow-env

nextflow run /home/guibo205/git/NBIS/Earth-Biogenome-Project-pilot $NEXTFLOW_OPTS \
    -profile uppmax,execution_report \
    --input assembly_parameters.yml \
    --outdir "${RESULTS}" \
    --project 'naiss2023-5-307'

nextflow clean -f -before $( nextflow log -q | tail -n 1 )

Expected behavior I expect asm.p_ctg.fa to be produced, as well as hap1 and hap2.

Screenshots

├── 03_assembly
│   └── null
│       ├── Gomphus_clavatus.asm.bp.hap1.p_ctg.assembly_summary
│       ├── Gomphus_clavatus.asm.bp.hap1.p_ctg.fasta.gz
│       ├── Gomphus_clavatus.asm.bp.hap1.p_ctg.gfa
│       ├── Gomphus_clavatus.asm.bp.hap1.p_ctg.gfa.gz
│       ├── Gomphus_clavatus.asm.bp.hap2.p_ctg.assembly_summary
│       ├── Gomphus_clavatus.asm.bp.hap2.p_ctg.fasta.gz
│       ├── Gomphus_clavatus.asm.bp.hap2.p_ctg.gfa
│       ├── Gomphus_clavatus.asm.bp.hap2.p_ctg.gfa.gz
│       ├── Gomphus_clavatus.asm.bp.p_utg.gfa
│       ├── Gomphus_clavatus.asm.bp.r_utg.gfa
│       ├── Gomphus_clavatus.asm.ec.bin
│       ├── Gomphus_clavatus.asm.ovlp.reverse.bin
│       └── Gomphus_clavatus.asm.ovlp.source.bin

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mahesh-panchal commented 7 months ago

It seems it's missing from the nf-core module. Submitted a patch: https://github.com/nf-core/modules/pull/4322

mahesh-panchal commented 7 months ago

Added via 9baf70a19925652493e5ddef3ea6dba7f77af02b to dev branch. The module will get updated from nf-core at a later date.