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Add nf-validation #272

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Add nf-validation

Add nf-validation #272

GitHub Actions / JUnit Test Report failed Mar 28, 2024 in 0s

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

Annotations

Check failure on line 1 in Run with profile test

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Run with profile test 

Assertion failed: 

1 of 6 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.02.0-edge
Launching `/home/runner/work/hic/hic/./tests/../main.nf` [compassionate_feynman] DSL2 - revision: 20e9605ae7
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                      : compassionate_feynman
  containerEngine              : docker
  launchDir                    : /home/runner/work/hic/hic/.nf-test/tests/d9eb59d4c36004c10649bc898fae0089
  workDir                      : /home/runner/work/hic/hic/.nf-test/tests/d9eb59d4c36004c10649bc898fae0089/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/d9eb59d4c36004c10649bc898fae0089/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

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`
[id:SRR4292758, single_end:false]
[83/b5b4ff] Submitted process > NFCORE_HIC:HIC:PREPARE_GENOME:BOWTIE2_BUILD (W303_SGD_2015_JRIU00000000.fsa)
[a6/da5e5a] Submitted process > NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS (A^AGCTT)
[60/b9a95f] Submitted process > NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (W303_SGD_2015_JRIU00000000.fsa)
[75/0d28f7] Submitted process > NFCORE_HIC:HIC:FASTQC (SRR4292758)
[7f/5f0153] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (W303_SGD_2015_JRIU00000000.fsa})
[7f/8cfc70] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (W303_SGD_2015_JRIU00000000.fsa})
[0b/6aea85] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[ac/2655df] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[02/1e7c14] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[22/79d2c3] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[bc/5bda92] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[d6/cb932b] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[76/c59c8f] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[1d/e98901] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[fb/bb4199] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS (SRR4292758)
[55/b5a77c] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS (SRR4292758)
[6e/ec854d] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES (SRR4292758)
[a6/d6b7c3] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS (SRR4292758)
[a8/7da812] Submitted process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION (SRR4292758)
[05/24658e] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS (SRR4292758)
[be/d6dfe8] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_VALID_INTERACTION (SRR4292758)
[39/aadbd2] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO2PAIRS (SRR4292758)
[fc/83f4ff] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_CLOAD (SRR4292758)
[2f/20fbf9] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_CLOAD (SRR4292758)
[b8/3f5265] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_BALANCE (SRR4292758)
[d8/451c82] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_ZOOMIFY (SRR4292758)
[58/44bf74] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_BALANCE (SRR4292758)
[c8/fdcde3] Submitted process > NFCORE_HIC:HIC:TADS:HIC_FIND_TADS (1)
[4d/117758] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_DUMP (SRR4292758)
[76/e457e3] Submitted process > NFCORE_HIC:HIC:TADS:COOLTOOLS_INSULATION (SRR4292758)
[15/5137a9] Submitted process > NFCORE_HIC:HIC:HIC_PLOT_DIST_VS_COUNTS (SRR4292758)
[a3/513f15] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_DUMP (SRR4292758)
[d2/b5b525] Submitted process > NFCORE_HIC:HIC:COMPARTMENTS:COOLTOOLS_EIGSCIS (SRR4292758)
[f0/015e02] Submitted process > NFCORE_HIC:HIC:COOLER:SPLIT_COOLER_DUMP (SRR4292758)
[85/ea8e62] Submitted process > NFCORE_HIC:HIC:COOLER:SPLIT_COOLER_DUMP (SRR4292758)
[07/7a4ae3] Submitted process > NFCORE_HIC:HIC:MULTIQC
-[nf-core/hic] Pipeline completed successfully-
Nextflow stderr:

Check failure on line 1 in Should split fastqs

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Should split fastqs 

Assertion failed: 

1 of 6 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.02.0-edge
Launching `/home/runner/work/hic/hic/./tests/../main.nf` [adoring_mcnulty] DSL2 - revision: 20e9605ae7
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                      : adoring_mcnulty
  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`
[cb/11ca07] Submitted process > NFCORE_HIC:HIC:PREPARE_GENOME:BOWTIE2_BUILD (W303_SGD_2015_JRIU00000000.fsa)
[f0/e70287] Submitted process > NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (W303_SGD_2015_JRIU00000000.fsa)
[98/caf214] Submitted process > NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS (A^AGCTT)
[ac/a905c8] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (W303_SGD_2015_JRIU00000000.fsa})
[72/52105b] 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]
[73/9c9677] Submitted process > NFCORE_HIC:HIC:FASTQC (SRR4292758)
[e8/81bbe8] Submitted process > NFCORE_HIC:HIC:FASTQC (SRR4292758)
[93/32a803] Submitted process > NFCORE_HIC:HIC:FASTQC (SRR4292758)
[fa/44decb] Submitted process > NFCORE_HIC:HIC:FASTQC (SRR4292758)
[de/4e827e] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[be/1946c9] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[74/f93406] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[11/714ead] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[25/88f771] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[18/836d4f] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[cf/a14fbf] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[c4/8c4a42] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (SRR4292758)
[7e/e9aa93] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[7a/fe07b4] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[05/bf74dc] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[82/a8f969] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[95/65b65e] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[ef/23b42f] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[0f/37f270] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[75/15f240] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[ce/4dd36d] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[fb/e17d1b] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[27/c445ab] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS (SRR4292758)
[a3/e3789a] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[f2/1204a4] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[0b/b1f703] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[65/1dc919] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[71/27aa35] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[44/84a721] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[9a/3882c3] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[3a/b61965] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED (SRR4292758)
[9e/a880d0] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[24/01c651] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[29/10664e] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[0d/62b6fc] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[6c/8166f8] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 (SRR4292758)
[cf/ab6e6c] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS (SRR4292758)
[17/c2f4ce] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS (SRR4292758)
[ff/8c74d3] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES (SRR4292758)
[5d/addbe3] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES (SRR4292758)
[e7/bbe5ec] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES (SRR4292758)
[0e/f58f38] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES (SRR4292758)
[c0/50852d] Submitted process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION (SRR4292758)
[55/6b6e4e] Submitted process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION (SRR4292758)
[23/9fb369] Submitted process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION (SRR4292758)
[95/ce57fb] Submitted process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION (SRR4292758)
[8b/8fe521] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS (SRR4292758)
[22/45be10] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS (SRR4292758)
[49/e0d251] Submitted process > NFCORE_HIC:HIC:HICPRO:MERGE_VALID_INTERACTION (SRR4292758)
[82/e46dc9] Submitted process > NFCORE_HIC:HIC:HICPRO:HICPRO2PAIRS (SRR4292758)
[66/325439] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_CLOAD (SRR4292758)
[fe/6cfc44] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_CLOAD (SRR4292758)
[29/8e64d8] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_ZOOMIFY (SRR4292758)
[92/bc24b8] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_BALANCE (SRR4292758)
[11/dbd14a] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_BALANCE (SRR4292758)
[0d/a093bb] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_DUMP (SRR4292758)
[c1/13f090] Submitted process > NFCORE_HIC:HIC:TADS:COOLTOOLS_INSULATION (SRR4292758)
[02/fc2690] Submitted process > NFCORE_HIC:HIC:HIC_PLOT_DIST_VS_COUNTS (SRR4292758)
[67/ba7c01] Submitted process > NFCORE_HIC:HIC:TADS:HIC_FIND_TADS (1)
[2c/9c1108] Submitted process > NFCORE_HIC:HIC:COOLER:COOLER_DUMP (SRR4292758)
[cc/151dc3] Submitted process > NFCORE_HIC:HIC:COMPARTMENTS:COOLTOOLS_EIGSCIS (SRR4292758)
[37/0e09a9] Submitted process > NFCORE_HIC:HIC:COOLER:SPLIT_COOLER_DUMP (SRR4292758)
[41/7f3230] Submitted process > NFCORE_HIC:HIC:COOLER:SPLIT_COOLER_DUMP (SRR4292758)
[96/df82de] Submitted process > NFCORE_HIC:HIC:MULTIQC
-[nf-core/hic] Pipeline completed successfully-
Nextflow stderr:
View more details on GitHub Actions