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nf-core / smrnaseq

A small-RNA sequencing analysis pipeline
https://nf-co.re/smrnaseq
MIT License
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NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN (1): Path value cannot be null #331

Closed vishal7245 closed 6 months ago

vishal7245 commented 7 months ago

Description of the bug

In the MIRDEEP2_RUN step, the pipeline is throwing error of work-dir=null error [nextflow.exception.ProcessUnrecoverableException]: Path value cannot be null

I have scanned through the pipeline subworkflows and modules and failed to understand the which work-dir, this error is talking about.

Also, this error is occuring at a stage where no work folder is being generated so there is no way to track command output or anything

[- ] process > NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN - there is no mention of work dir assigned to this step

Command used and terminal output

[Input]
nextflow run nf-core/smrnaseq -r dev -profile singularity -params-file nf-params.json

[Output]
N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/nf-core/smrnaseq` [serene_visvesvaraya] DSL2 - revision: d5910ecbe7 [dev]
WARN: Running with Protocol illumina
WARN: Therefore using Adapter: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
WARN: Clipping 0 bases from R1
WARN: And clipping 0 bases from 3' end
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/smrnaseq v2.3.1dev-gd5910ec
------------------------------------------------------
Core Nextflow options
  revision        : dev
  runName         : serene_visvesvaraya
  containerEngine : singularity
  launchDir       : /media/vishal/345CBF8B7CA2CB42/virdb_rna/test
  workDir         : /media/vishal/345CBF8B7CA2CB42/virdb_rna/test/work
  projectDir      : /home/vishal/.nextflow/assets/nf-core/smrnaseq
  userName        : vishal
  profile         : singularity
  configFiles     : 

Input/output options
  input           : /media/vishal/345CBF8B7CA2CB42/virdb_rna/test/datasheet.csv
  outdir          : /media/vishal/345CBF8B7CA2CB42/virdb_rna/test/new_approach

Reference genome options
  genome          : GRCh37
  mirtrace_species: hsa
  fasta           : /media/vishal/345CBF8B7CA2CB42/virdb_rna/test/GCF_000001405.40_GRCh38.p14_genomic.fna

Max job request options
  max_memory      : 30.GB

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/smrnaseq for your analysis please cite:

* The pipeline
  10.5281/zenodo.3456879

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/smrnaseq/blob/master/CITATIONS.md
------------------------------------------------------
[-        ] process > NFCORE_SMRNASEQ:CAT_FASTQ                                                                 -
[-        ] process > NFCORE_SMRNASEQ:CAT_FASTQ                                                                 -
[ee/08431b] process > NFCORE_SMRNASEQ:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW (non-segmental-vitiligo_8)         [100%] 20 of 20, cached: 20 ✔
[cd/5d579f] process > NFCORE_SMRNASEQ:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP (non-segmental-vitiligo_10)             [100%] 20 of 20, cached: 20 ✔
[e2/fcfd70] process > NFCORE_SMRNASEQ:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM (Healthy_6)                       [100%] 1 of 1, cached: 1
[31/f63421] process > NFCORE_SMRNASEQ:INDEX_GENOME (GCF_000001405.40_GRCh38.p14_genomic.fna)                    [100%] 1 of 1, cached: 1 ✔
[-        ] process > NFCORE_SMRNASEQ:MIRTRACE:MIRTRACE_RUN                                                     -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:PARSE_MATURE                                                  -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:FORMAT_MATURE                                                 -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:INDEX_MATURE                                                  -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_MATURE                                             -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:SAMTOOLS_SORT                                -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:SAMTOOLS_INDEX                               -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS            -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT         -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS         -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:PARSE_HAIRPIN                                                 -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:FORMAT_HAIRPIN                                                -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:INDEX_HAIRPIN                                                 -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_HAIRPIN                                            -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:SAMTOOLS_SORT                               -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:SAMTOOLS_INDEX                              -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS           -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT        -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS        -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:EDGER_QC                                                      -
[8f/a78be6] process > NFCORE_SMRNASEQ:MIRNA_QUANT:SEQCLUSTER_SEQUENCES (Healthy_6_seqcluster)                   [100%] 1 of 1, cached: 1
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_SEQCLUSTER                                         -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT                                                  -
[-        ] process > NFCORE_SMRNASEQ:MIRNA_QUANT:TABLE_MERGE                                                   -
[-        ] process > NFCORE_SMRNASEQ:GENOME_QUANT:BOWTIE_MAP_GENOME                                            -
[-        ] process > NFCORE_SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                        -
[-        ] process > NFCORE_SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                       -
[-        ] process > NFCORE_SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS    -
[-        ] process > NFCORE_SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[-        ] process > NFCORE_SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[af/d30473] process > NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_PIGZ (Healthy_6)                                        [100%] 1 of 1, cached: 1
[af/a89cb7] process > NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_MAPPER (Healthy_6)                                      [100%] 1 of 1, cached: 1
[-        ] process > NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN                                                     -
[-        ] process > NFCORE_SMRNASEQ:MULTIQC                                                                   -
WARN: Input tuple does not match input set cardinality declared by process `NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN` -- offending value: https://mirbase.org/download/hairpin.fa
ERROR ~ Error executing process > 'NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN (1)'

Caused by:
  Path value cannot be null

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details

Relevant files

.nextflow.log datasheet.csv nf-params.json

System information

Nextflow version: 23.10.1 Hardware: Desktop Executor: Local Container engine: Singularity Version of nf-core/smrnaseq: dev

christopher-mohr commented 7 months ago

There seems to be an issue with the input channels of the module that might also be related to your issue.

WARN: Input tuple does not match input set cardinality declared by process NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN -- offending value: https://mirbase.org/download/hairpin.fa

Definieitly something we should fix.

chuan-wang commented 7 months ago

A temp solution:

Modify workflow/modules/local/mirdeep2_run.nf lines 15-16 from

tuple val(meta2), path(hairpin)
tuple val(meta2), path(mature)

into

path(hairpin)
path(mature)
christopher-mohr commented 7 months ago

Hi @vishal7245, can you test it again with the current dev branch version?

christopher-mohr commented 6 months ago

Please reopen if the problem persists.