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--sample alias not reflected in output file names #58

Closed hackkr closed 6 months ago

hackkr commented 6 months ago

Operating System

Other Linux (please specify below)

Other Linux

GNOME Terminal 3.28.3

Workflow Version

v1.1.0

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-pore-c --fastq 01_poreC_test/ont_files/fastq_pass --ref GCF_000189555.1_ASM18955v1_genomic.fna --cutter AluI --out_dir 01_poreC_test/wf-output2 -profile singularity --pairs True --sample sis

Workflow Execution - CLI Execution Profile

None

What happened?

Wf-pore-C is running without error. However, when I provide a sample alias, the only output files with the alias correctly integrated is the filtered_out.bam file. All other outputs are named "null" in place of the provided sample name. This issue is also present when I run the demo data.

Relevant log output

N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/epi2me-labs/wf-pore-c` [fabulous_torricelli] DSL2 - revision: a4ffadaaa9 [master]

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-pore-c v1.1.0-ga4ffada
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : fabulous_torricelli
  containerEngine: singularity
  container      : [withLabel:wfporec:ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0, withLabel:pore_c_py:ontresearch/pore-c-py:shad5608368dcce93646de5559f2f391005408da6c2, withLabel:wf_common:ontresearch/wf-common:sha1c5febff9f75143710826498b093d9769a5edbb9]
  launchDir      : /N/slate/rhackley/01_poreC_test
  workDir        : /N/slate/rhackley/01_poreC_test/work
  projectDir     : /N/u/rhackley/Quartz/.nextflow/assets/epi2me-labs/wf-pore-c
  userName       : rhackley
  profile        : singularity
  configFiles    : /N/u/rhackley/Quartz/.nextflow/assets/epi2me-labs/wf-pore-c/nextflow.config

Input Options
  fastq          : /N/slate/rhackley/01_poreC_test/ont_files/fastq_pass
  sample         : sis
  ref            : /N/slate/rhackley/000_genomes_genes/sulf_isl_dataset/GCF_000189555.1/GCF_000189555.1_ASM18955v1_genomic.fna
  cutter         : AluI

Output Options
  out_dir        : /N/slate/rhackley/01_poreC_test/wf-output2
  hi_c           : true

Pore-C Tools Options
  coverage       : true

Chromunity Options
  chromunity     : true

4DN files Options
  pairs          : true
  mcool          : true

!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-pore-c for your analysis please cite:

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

--------------------------------------------------------------------------------
This is epi2me-labs/wf-pore-c v1.1.0-ga4ffada.
--------------------------------------------------------------------------------
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
[-        ] process > POREC:fastcat                      -
executor >  local (2)
[f7/eab15f] process > POREC:fastcat (1)                      [  0%] 0 of 1
executor >  local (5)
[f7/eab15f] process > POREC:fastcat (1)                      [  0%] 0 of 1
executor >  local (5)
[f7/eab15f] process > POREC:fastcat (1)                      [  0%] 0 of 1
executor >  local (5)
[f7/eab15f] process > POREC:fastcat (1)                      [  0%] 0 of 1
executor >  local (5)
[f7/eab15f] process > POREC:fastcat (1)                      [  0%] 0 of 1
executor >  local (5)
[f7/eab15f] process > POREC:fastcat (1)                      [  0%] 0 of 1
executor >  local (8)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (8)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (8)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (9)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (12)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (13)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (13)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (14)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (15)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (16)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (17)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (18)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (19)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (20)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (21)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (22)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (23)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (24)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (24)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (25)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (26)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (27)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (27)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (28)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (29)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (29)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (30)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (30)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (30)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (31)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (32)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (32)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (34)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (34)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (35)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (38)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (38)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (39)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (40)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (40)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (41)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (41)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (43)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (43)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (43)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (45)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (46)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (47)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (48)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (49)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (49)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (50)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (51)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (51)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (52)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (54)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (55)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (56)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (57)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (57)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (58)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (59)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (59)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (60)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (60)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (61)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (61)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (62)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (62)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (63)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (64)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (64)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (65)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (65)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (67)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (69)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (71)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (72)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (74)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (74)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (75)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (75)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (75)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (77)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (77)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (78)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (78)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (79)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (80)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (81)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (81)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (81)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (81)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (82)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (82)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (82)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (82)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (82)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (82)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (82)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (83)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (83)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (84)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (84)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (84)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (85)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (85)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (85)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (85)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
executor >  local (85)
[f7/eab15f] process > POREC:fastcat (1)                      [100%] 1 of 1 ✔
[c2/6540c3] process > POREC:index_bam (1)                    [100%] 1 of 1 ✔
[3d/861688] process > POREC:prepare_genome:index_ref_fai (1) [100%] 1 of 1 ✔
[76/deeb04] process > POREC:prepare_genome:index_ref_mmi (1) [100%] 1 of 1 ✔
[91/87f99c] process > POREC:digest_align_annotate (16)       [100%] 22 of 22 ✔
[-        ] process > POREC:haplotag_alignments              -
[cb/b05331] process > POREC:merge_coordsorted_bams (1)       [100%] 1 of 1 ✔
[8d/3ae735] process > POREC:merge_namesorted_bams (1)        [100%] 1 of 1 ✔
[de/44647b] process > POREC:create_restriction_bed (1)       [100%] 1 of 1 ✔
[51/1fb76e] process > POREC:mosdepth_coverage (1)            [100%] 1 of 1 ✔
[5d/69a151] process > POREC:to_pairs_file (22)               [100%] 22 of 22 ✔
[0d/6188f7] process > POREC:pairsToCooler (21)               [100%] 22 of 22 ✔
[2c/266b9d] process > POREC:merge_mcools (1)                 [100%] 1 of 1 ✔
[45/751eda] process > POREC:merge_pairs (1)                  [100%] 1 of 1 ✔
[6f/2a3e3e] process > POREC:merge_pairs_stats (1)            [100%] 1 of 1 ✔
[53/faa337] process > POREC:pair_stats_report (1)            [100%] 1 of 1 ✔
[70/6371fd] process > POREC:merge_parquets_to_dataset (1)    [100%] 1 of 1 ✔
[e2/566972] process > POREC:getVersions                      [100%] 1 of 1 ✔
[2c/dfcda6] process > POREC:getParams                        [100%] 1 of 1 ✔
[5b/71ee21] process > POREC:makeReport                       [100%] 1 of 1 ✔
[da/7a5165] process > POREC:prepare_hic (1)                  [100%] 1 of 1 ✔
[2b/cfedeb] process > POREC:get_filtered_out_bam (1)         [100%] 1 of 1 ✔
[d7/d0e7c6] process > output (1)                             [100%] 1 of 1 ✔
Completed at: 26-Apr-2024 16:44:34
Duration    : 5m 31s
CPU hours   : 1.3
Succeeded   : 85

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

sarahjeeeze commented 6 months ago

Hi, Thanks for pointing this out we will ensure all the outputs are clearly named with the sample alias in the next release.