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Add nf-validation #276

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Add nf-validation

Add nf-validation #276

GitHub Actions / JUnit Test Report failed Apr 9, 2024 in 0s

2 tests run, 1 passed, 0 skipped, 1 failed.

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Check failure on line 1 in Should split fastqs

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@github-actions github-actions / JUnit Test Report

Should split fastqs 

Assertion failed: 

1 of 16 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/hic/hic/./tests/../main.nf` [jolly_minsky] DSL2 - revision: 20e9605ae7
WARN: A process with name 'BOWTIE2_ALIGN_TRIMMED' is defined more than once in module script: /home/runner/work/hic/hic/./workflows/../subworkflows/local/./hicpro_mapping.nf -- Make sure to not define the same function as process
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/hic v2.2.0dev
------------------------------------------------------
Core Nextflow options
  runName                      : jolly_minsky
  containerEngine              : docker
  launchDir                    : /home/runner/work/hic/hic/.nf-test/tests/6b19ffdc5efbfed82ee2c8ffb61bd299
  workDir                      : /home/runner/work/hic/hic/.nf-test/tests/6b19ffdc5efbfed82ee2c8ffb61bd299/work
  projectDir                   : /home/runner/work/hic/hic
  userName                     : runner
  profile                      : docker
  configFiles                  : 

Input/output options
  input                        : /home/runner/work/hic/hic/assets/samplesheet.csv
  outdir                       : /home/runner/work/hic/hic/.nf-test/tests/6b19ffdc5efbfed82ee2c8ffb61bd299/output

Reference genome options
  fasta                        : https://github.com/nf-core/test-datasets/raw/hic/reference/W303_SGD_2015_JRIU00000000.fsa

Digestion Hi-C
  digestion                    : hindiii

DNAse Hi-C
  min_cis_dist                 : 0

Alignments
  split_fastq                  : true
  fastq_chunks_size            : 125000

Valid Pairs Detection
  max_insert_size              : 0
  min_insert_size              : 0
  max_restriction_fragment_size: 0
  min_restriction_fragment_size: 0

Contact maps
  bin_size                     : 2000,1000
  ice_filter_high_count_perc   : 0

Downstream Analysis
  res_dist_decay               : 1000
  tads_caller                  : insulation,hicexplorer
  res_tads                     : 1000
  res_compartments             : 2000

Institutional config options
  config_profile_name          : Hi-C test data from Schalbetter et al. (2017)
  config_profile_description   : Minimal test dataset to check pipeline function

Max job request options
  max_cpus                     : 2
  max_memory                   : 4 GB
  max_time                     : 1h

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

* The pipeline
  10.5281/zenodo.2669512

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

* Software dependencies
  https://github.com/nf-core/hic/blob/master/CITATIONS.md
------------------------------------------------------
WARN: The following invalid input values have been detected:

* --digest: [hindiii:[restriction_site:A^AGCTT, ligation_site:AAGCTAGCTT], mboi:[restriction_site:^GATC, ligation_site:GATCGATC], dpnii:[restriction_site:^GATC, ligation_site:GATCGATC], arima:[restriction_site:^GATC,G^ANTC, ligation_site:GATCGATC,GATCANTC,GANTGATC,GANTANTC], arimaV2:[restriction_site:^GATC,G^ANTC,C^TNAG,T^TAA, ligation_site:GATCGATC,GATCANTC,GANTGATC,GANTANTC,GATCTNAG,GANTTNAG,CTNAGATC,CTNAANTC,TTAGATC,TTAANTC,TTATTNAG,GATCTAA,GANTTAA,CTNATAA,TTATAA,CTNATNAG]]
* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/
* --pipelines_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/
* --schema_ignore_params: genomes,digest,input_paths,input


WARN: Access to undefined parameter `bwt2_index` -- Initialise it to a default value eg. `params.bwt2_index = some_value`
[2e/bc26a5] Submitted process > NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (W303_SGD_2015_JRIU00000000.fsa)
[a9/3e3234] Submitted process > NFCORE_HIC:HIC:PREPARE_GENOME:BOWTIE2_BUILD (W303_SGD_2015_JRIU00000000.fsa)
[e1/4bfcb0] Submitted process > NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS (A^AGCTT)
[06/54ff08] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (W303_SGD_2015_JRIU00000000.fsa})
[2b/842861] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (W303_SGD_2015_JRIU00000000.fsa})
[id:SRR4292758, single_end:false]
[id:SRR4292758, single_end:false]
[id:SRR4292758, single_end:false]
[id:SRR4292758, single_end:false]
[66/7b03ab] Submitted process > NFCORE_HIC:HIC:FASTQC (SRR4292758)
[d4/104106] Submitted process > NFCORE_HIC:HIC:FASTQC (SRR4292758)
[72/70b415] Submitted process > NFCORE_HIC:HIC:FASTQC (SRR4292758)
[73/f29cb6] Submitted process > NFCORE_HIC:HIC:FASTQC (SRR4292758)
[9a/20010a] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[b6/ca1925] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[a5/afd1b3] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[eb/3a59a6] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[4e/be5f04] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[52/8f523d] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[3f/bf36eb] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[fd/b79967] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[2a/6a234f] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[09/eeb3ae] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[af/a74fea] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[89/a2e67e] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[4a/cf68da] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[cc/585bfa] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[19/1ac18e] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[8c/54cbe3] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[db/930d94] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[5f/e3623d] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[01/834d74] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[33/23888e] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[5e/1bd0da] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[ae/786828] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[7a/a5ebcc] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[92/01eba9] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[8a/72dec8] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[87/017299] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[41/81df35] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[13/285626] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[4b/7e7ae6] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[b1/e8e5b3] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[72/f40ff0] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[ee/89bd79] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[d8/e3e8bd] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS (SRR4292758)
[28/45ca26] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS (SRR4292758)
[71/5ae054] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES (SRR4292758)
[9d/0e9d71] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES (SRR4292758)
[36/6ab062] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES (SRR4292758)
[9b/ba87e0] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES (SRR4292758)
[5e/f4938c] Submitted process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION (SRR4292758)
[1a/138216] Submitted process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION (SRR4292758)
[91/d47485] Submitted process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION (SRR4292758)
[b4/1b4114] Submitted process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION (SRR4292758)
[2b/caed99] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS (SRR4292758)
[cc/ce45d1] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS (SRR4292758)
[00/7a0bd5] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_VALID_INTERACTION (SRR4292758)
[0f/1316f2] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO2PAIRS (SRR4292758)
[36/fa38f6] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_CLOAD (SRR4292758)
[ca/c34a1d] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_CLOAD (SRR4292758)
[64/df023f] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_BALANCE (SRR4292758)
[7d/7a6314] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_ZOOMIFY (SRR4292758)
[25/419f42] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_BALANCE (SRR4292758)
[08/931743] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_DUMP (SRR4292758)
[97/0384ce] Submitted process > NFCORE_HIC:HIC:COMPARTMENTS:COOLTOOLS_EIGSCIS (SRR4292758)
[ed/536262] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_DUMP (SRR4292758)
[70/01e76b] Submitted process > NFCORE_HIC:HIC:HIC_PLOT_DIST_VS_COUNTS (SRR4292758)
[6d/a66f18] Submitted process > NFCORE_HIC:HIC:TADS:COOLTOOLS_INSULATION (SRR4292758)
[ab/0e15a2] Submitted process > NFCORE_HIC:HIC:TADS:HIC_FIND_TADS (1)
[a2/852e82] Submitted process > NFCORE_HIC:HIC:COOLER:SPLIT_COOLER_DUMP (SRR4292758)
[6e/1d025d] Submitted process > NFCORE_HIC:HIC:COOLER:SPLIT_COOLER_DUMP (SRR4292758)
[b5/23f068] Submitted process > NFCORE_HIC:HIC:MULTIQC
-[nf-core/hic] Pipeline completed successfully-
Nextflow stderr:
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