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Make genomic FASTA input optional #236

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Make genomic FASTA input optional

Make genomic FASTA input optional #236

GitHub Actions / JUnit Test Report failed Jan 22, 2025 in 0s

3 tests run, 0 passed, 0 skipped, 3 failed.

Annotations

Check failure on line 1 in Test pipeline with dummy UMI settings

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline with dummy UMI settings.Params: --aligner hisat2 --umi_dedup_tool 'umicollapse' 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.12.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [hungry_stone] DSL2 - revision: 85c9b75b8b
Downloading plugin [email protected]

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq 3.19.0dev
------------------------------------------------------
Input/output options
  input                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv
  outdir                      : /home/runner/work/rnaseq/rnaseq/~/tests/f49e8b94b0809135bf4a29582123097b/output

Reference genome options
  fasta                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genome.fasta
  gtf                         : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes_with_empty_tid.gtf.gz
  gff                         : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz
  transcript_fasta            : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta
  additional_fasta            : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz
  hisat2_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz
  rsem_index                  : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz
  salmon_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz
  hisat2_build_memory         : 3.GB

Read filtering options
  bbsplit_fasta_list          : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt

UMI options
  with_umi                    : true
  umi_dedup_tool              : umicollapse
  umitools_extract_method     : regex
  umitools_bc_pattern         : ^(?P<umi_1>CGA.{8}){s<=2}.*
  umitools_dedup_stats        : true

Alignment options
  aligner                     : hisat2
  pseudo_aligner              : salmon

Optional outputs
  save_umi_intermeds          : true

Institutional config options
  config_profile_name         : Test profile
  config_profile_description  : Minimal test dataset to check pipeline function

Generic options
  pipelines_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/

Core Nextflow options
  runName                     : hungry_stone
  containerEngine             : docker
  launchDir                   : /home/runner/work/rnaseq/rnaseq/~/tests/f49e8b94b0809135bf4a29582123097b
  workDir                     : /home/runner/work/rnaseq/rnaseq/~/tests/f49e8b94b0809135bf4a29582123097b/work
  projectDir                  : /home/runner/work/rnaseq/rnaseq
  userName                    : runner
  profile                     : test,docker
  configFiles                 : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    https://doi.org/10.5281/zenodo.1400710

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

* Software dependencies
    https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md

WARN: The following invalid input values have been detected:

* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/


WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Both '--gtf' and '--gff' parameters have been provided.
  Using GTF file as priority.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  '--transcript_fasta' parameter has been provided.
  Make sure transcript names in this file match those in the GFF/GTF file.

  Please see:
  https://github.com/nf-core/rnaseq/issues/753
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  When using '--additional_fasta <FASTA_FILE>' the aligner index will not
  be re-built with the transgenes incorporated by default since you have 
  already provided an index via '--hisat2_index <INDEX>'.

  Set '--additional_fasta <FASTA_FILE> --hisat2_index false --gene_bed false --save_reference'
  to re-build the index with transgenes included and the index and gene BED file will be saved in
  'results/genome/index/hisat2/' for re-use with '--hisat2_index'.

  Ignore this warning if you know that the index already contains transgenes.

  Please see:
  https://github.com/nf-core/rnaseq/issues/556
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[cc/fac6ef] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[b8/9da3ea] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[4e/f861d2] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)
ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)'

Caused by:
  Process `NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)` terminated with an error exit status (126)


Command executed:

  # Not calling gunzip itself because it creates files
  # with the original group ownership rather than the
  # default one for that user / the work directory
  gzip \
      -cd \
       \
      genes_with_empty_tid.gtf.gz \
      > genes_with_empty_tid.gtf
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF":
      gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*$//')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/nf-core/ubuntu:22.04' locally
  22.04: Pulling from nf-core/ubuntu
  9b857f539cb1: Pulling fs layer
  9b857f539cb1: Verifying Checksum
  9b857f539cb1: Download complete
  9b857f539cb1: Pull complete
  Digest: sha256:bd1487129c4e01470664c3f3c9a25ce01f73ff3df75ffa7eb3388d3d4b945369
  Status: Image is up to date for quay.io/nf-core/ubuntu:22.04
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/f49e8b94b0809135bf4a29582123097b/work/b8/9da3ea90adcc344a671f8ef1e830b8

Container:
  quay.io/nf-core/ubuntu:22.04

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/f49e8b94b0809135bf4a29582123097b/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/f49e8b94b0809135bf4a29582123097b/meta/nextflow.log' file for details
-[nf-core/rnaseq] Pipeline completed with errors-
Nextflow stderr:

Check failure on line 1 in Test pipeline with dummy UMI settings

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline with dummy UMI settings.--umi_dedup_tool 'umitools' 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.12.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [compassionate_faraday] DSL2 - revision: 85c9b75b8b

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq 3.19.0dev
------------------------------------------------------
Input/output options
  input                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv
  outdir                      : /home/runner/work/rnaseq/rnaseq/~/tests/6ab87d34b6527c3696e35b350986c2a2/output

Reference genome options
  fasta                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genome.fasta
  gtf                         : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes_with_empty_tid.gtf.gz
  gff                         : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz
  transcript_fasta            : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta
  additional_fasta            : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz
  hisat2_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz
  rsem_index                  : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz
  salmon_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz
  hisat2_build_memory         : 3.GB

Read filtering options
  bbsplit_fasta_list          : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt

UMI options
  with_umi                    : true
  umitools_extract_method     : regex
  umitools_bc_pattern         : ^(?P<umi_1>CGA.{8}){s<=2}.*
  umitools_dedup_stats        : true

Alignment options
  pseudo_aligner              : salmon

Optional outputs
  save_umi_intermeds          : true

Institutional config options
  config_profile_name         : Test profile
  config_profile_description  : Minimal test dataset to check pipeline function

Generic options
  pipelines_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/

Core Nextflow options
  runName                     : compassionate_faraday
  containerEngine             : docker
  launchDir                   : /home/runner/work/rnaseq/rnaseq/~/tests/6ab87d34b6527c3696e35b350986c2a2
  workDir                     : /home/runner/work/rnaseq/rnaseq/~/tests/6ab87d34b6527c3696e35b350986c2a2/work
  projectDir                  : /home/runner/work/rnaseq/rnaseq
  userName                    : runner
  profile                     : test,docker
  configFiles                 : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    https://doi.org/10.5281/zenodo.1400710

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

* Software dependencies
    https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md

WARN: The following invalid input values have been detected:

* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/


WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Both '--gtf' and '--gff' parameters have been provided.
  Using GTF file as priority.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  '--transcript_fasta' parameter has been provided.
  Make sure transcript names in this file match those in the GFF/GTF file.

  Please see:
  https://github.com/nf-core/rnaseq/issues/753
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[fc/639592] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT (RAP1_UNINDUCED_REP1)
[b0/417195] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[b2/3fb696] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)
ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)'

Caused by:
  Process `NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)` terminated with an error exit status (126)


Command executed:

  # Not calling gunzip itself because it creates files
  # with the original group ownership rather than the
  # default one for that user / the work directory
  gzip \
      -cd \
       \
      gfp.fa.gz \
      > gfp.fa
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA":
      gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*$//')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/6ab87d34b6527c3696e35b350986c2a2/work/b0/41719509f6deb783fc261e60467146

Container:
  quay.io/nf-core/ubuntu:22.04

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/6ab87d34b6527c3696e35b350986c2a2/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/6ab87d34b6527c3696e35b350986c2a2/meta/nextflow.log' file for details
ERROR ~ Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null

 -- Check script '/home/runner/work/rnaseq/rnaseq/./subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/utils_nfcore_pipeline/main.nf' at line: 97 or see '/home/runner/work/rnaseq/rnaseq/~/tests/6ab87d34b6527c3696e35b350986c2a2/meta/nextflow.log' file for more details
-[nf-core/rnaseq] Pipeline completed with errors-
WARN: Killing running tasks (2)
Nextflow stderr:

Check failure on line 1 in Test pipeline with dummy UMI settings

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline with dummy UMI settings.--umi_dedup_tool 'umitools - stub 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.12.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [insane_pauling] DSL2 - revision: 85c9b75b8b

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq 3.19.0dev
------------------------------------------------------
Input/output options
  input                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv
  outdir                      : /home/runner/work/rnaseq/rnaseq/~/tests/f6377de256b0bba1c086e98baa569e66/output

Reference genome options
  fasta                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genome.fasta
  gtf                         : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes_with_empty_tid.gtf.gz
  gff                         : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz
  transcript_fasta            : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta
  additional_fasta            : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz
  hisat2_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz
  rsem_index                  : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz
  salmon_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz
  hisat2_build_memory         : 3.GB

Read filtering options
  bbsplit_fasta_list          : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt

UMI options
  with_umi                    : true
  umitools_extract_method     : regex
  umitools_bc_pattern         : ^(?P<umi_1>CGA.{8}){s<=2}.*
  umitools_dedup_stats        : true

Alignment options
  pseudo_aligner              : salmon

Process skipping options
  skip_bbsplit                : false

Institutional config options
  config_profile_name         : Test profile
  config_profile_description  : Minimal test dataset to check pipeline function

Generic options
  pipelines_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/

Core Nextflow options
  runName                     : insane_pauling
  containerEngine             : docker
  launchDir                   : /home/runner/work/rnaseq/rnaseq/~/tests/f6377de256b0bba1c086e98baa569e66
  workDir                     : /home/runner/work/rnaseq/rnaseq/~/tests/f6377de256b0bba1c086e98baa569e66/work
  projectDir                  : /home/runner/work/rnaseq/rnaseq
  userName                    : runner
  profile                     : test,docker
  configFiles                 : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    https://doi.org/10.5281/zenodo.1400710

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

* Software dependencies
    https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md

WARN: The following invalid input values have been detected:

* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/


WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected.
HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.

WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Both '--gtf' and '--gff' parameters have been provided.
  Using GTF file as priority.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  '--transcript_fasta' parameter has been provided.
  Make sure transcript names in this file match those in the GFF/GTF file.

  Please see:
  https://github.com/nf-core/rnaseq/issues/753
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[0a/ac5c57] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[d6/9dc47d] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[50/574878] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)'

Caused by:
  Process `NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)` terminated with an error exit status (126)


Command executed:

  touch gfp.fa
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA":
      gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*$//')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/f6377de256b0bba1c086e98baa569e66/work/d6/9dc47d38e52f29f75885383be6b327

Container:
  quay.io/nf-core/ubuntu:22.04

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/f6377de256b0bba1c086e98baa569e66/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/f6377de256b0bba1c086e98baa569e66/meta/nextflow.log' file for details
-[nf-core/rnaseq] Pipeline completed with errors-
Nextflow stderr:
View more details on GitHub Actions