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Hi, has anyone tried running this pipeline with th...
# methylseq
m
Hi, has anyone tried running this pipeline with the test data recently? I think there may be an issue (see thread).
Command run:
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nextflow run nf-core/methylseq -r 2.6.0 -c nextflow.config -profile singularity,test --outdir results_methylseq
Output:
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------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/methylseq v2.6.0-g54f823e
------------------------------------------------------
Core Nextflow options
  revision                  : 2.6.0
  runName                   : peaceful_gauss
  containerEngine           : singularity
  launchDir                 : /ibex/user/pampum/2024-08-29_nextflow-test
  workDir                   : /ibex/user/pampum/2024-08-29_nextflow-test/work
  projectDir                : /home/pampum/.nextflow/assets/nf-core/methylseq
  userName                  : pampum
  profile                   : singularity,test
  configFiles               :

Input/output options
  input                     : /home/pampum/.nextflow/assets/nf-core/methylseq/assets/samplesheet.csv
  outdir                    : results_methylseq

Reference genome options
  fasta                     : <https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/reference/genome.fa>
  fasta_index               : <https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/reference/genome.fa.fai>
  igenomes_base             : <s3://ngi-igenomes/igenomes/>

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

Max job request options
  max_cpus                  : 2
  max_memory                : 6 GB
  max_time                  : 6h

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

* The pipeline
  <https://doi.org/10.5281/zenodo.1343417>

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

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

[-        ] NFCORE_METHYLSEQ:METHYLSEQ:PREPARE_GENOME:BISMARK_GENOMEPREPARATION -
ERROR ~ ERROR: Validation of '/home/pampum/.nextflow/assets/nf-core/methylseq/assets/samplesheet.csv' file failed!

 -- Check '.nextflow.log' file for details
The following errors have been detected:

* -- Entry 4 - fastq_1: the file or directory '<https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz>' does not exist.

 -- Check script '/home/pampum/.nextflow/assets/nf-core/methylseq/./workflows/methylseq.nf' at line: 89 or see '.nextflow.log' file for more details
m
file exist, can you check again?
m
Error still exists, with a different file this time
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[-        ] NFCORE_METHYLSEQ:METHYLSEQ:PREPARE_GENOME:BISMARK_GENOMEPREPARATION -
ERROR ~ ERROR: Validation of '/home/pampum/.nextflow/assets/nf-core/methylseq/assets/samplesheet.csv' file failed!

 -- Check '.nextflow.log' file for details
The following errors have been detected:

* -- Entry 4 - fastq_2: the file or directory '<https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz>' does not exist.
m
that not the same file anymore
Can you see if you can download the file with wget or curl?
m
yes 
wget <https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz>
works
m
ok
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