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docs: updated CHANGELOG

docs: updated CHANGELOG #1218

GitHub Actions / JUnit Test Report failed Mar 1, 2025 in 0s

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

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nf.test-dataset_simpleaf_aligner 

Assertion failed: 

11 of 16 assertions failed
Raw output 
Nextflow stdout:

ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:SIMPLEAF:SIMPLEAF_QUANT (Sample_Y)'

Caused by:
  Process `NFCORE_SCRNASEQ:SCRNASEQ:SIMPLEAF:SIMPLEAF_QUANT (Sample_Y)` terminated with an error exit status (1)


Command executed:

  # export required var
  export ALEVIN_FRY_HOME=.
  
  # prep simpleaf
  simpleaf set-paths
  
  # run simpleaf quant
  simpleaf quant \
      --t2g-map t2g_3col.tsv \
      --chemistry 10xv2 \
      --index index \
      --reads1 Sample_Y_S1_L001_R1_001.fastq.gz,Sample_Y_S1_L002_R1_001.fastq.gz \
      --reads2 Sample_Y_S1_L001_R2_001.fastq.gz,Sample_Y_S1_L002_R2_001.fastq.gz \
      --resolution cr-like \
      --output simpleaf_quant \
      --threads 2 \
      --anndata-out \
      --unfiltered-pl 10x_V2_barcode_whitelist.txt.gz \
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SCRNASEQ:SCRNASEQ:SIMPLEAF:SIMPLEAF_QUANT":
      alevin-fry: $(alevin-fry --version | sed -e "s/alevin-fry //g")
      piscem: $(piscem --version | sed -e "s/piscem //g")
      salmon: $(salmon --version | sed -e "s/salmon //g")
      simpleaf: $(simpleaf --version | sed -e "s/simpleaf //g")
  END_VERSIONS

Command exit status:
  1

Command output:
  found `piscem` in the PATH at /usr/local/bin/piscem
  found `salmon` in the PATH at /usr/local/bin/salmon
  found `alevin-fry` in the PATH at /usr/local/bin/alevin-fry
  2025-03-01T01:54:56.659805Z  INFO simpleaf::utils::prog_utils: Could not find macs3 executable, peak calling cannot be peformed by simpleaf
  2025-03-01T01:54:56.737143Z  INFO simpleaf::simpleaf_commands::quant: found file compressed using Gzip
  2025-03-01T01:54:56.737276Z  INFO simpleaf::simpleaf_commands::quant: piscem map-sc cmd : /usr/local/bin/piscem map-sc --index index/piscem_idx --threads 2 -o simpleaf_quant/af_map --max-ec-card 4096 --skipping-strategy permissive --max-hit-occ 256 --max-hit-occ-recover 1024 --max-read-occ 2500 -1 Sample_Y_S1_L001_R1_001.fastq.gz,Sample_Y_S1_L002_R1_001.fastq.gz -2 Sample_Y_S1_L001_R2_001.fastq.gz,Sample_Y_S1_L002_R2_001.fastq.gz --geometry chromium_v2
  2025-03-01T01:54:58.738656Z  INFO simpleaf::utils::prog_utils: command returned successfully (exit status: 0)
  2025-03-01T01:54:58.738690Z  INFO simpleaf::simpleaf_commands::quant: alevin-fry generate-permit-list cmd : /usr/local/bin/alevin-fry generate-permit-list -i simpleaf_quant/af_map -d fw --unfiltered-pl 10x_V2_barcode_whitelist.txt.gz --min-reads 10 -o simpleaf_quant/af_quant
  2025-03-01T01:54:58.997685Z  INFO simpleaf::utils::prog_utils: command returned successfully (exit status: 0)
  2025-03-01T01:54:58.997766Z  INFO simpleaf::simpleaf_commands::quant: alevin-fry collate cmd : /usr/local/bin/alevin-fry collate -i simpleaf_quant/af_quant -r simpleaf_quant/af_map -t 2
  2025-03-01T01:54:59.006392Z  INFO simpleaf::utils::prog_utils: command returned successfully (exit status: 0)
  2025-03-01T01:54:59.006608Z  INFO simpleaf::simpleaf_commands::quant: cmd : "/usr/local/bin/alevin-fry" "quant" "-i" "simpleaf_quant/af_quant" "-o" "simpleaf_quant/af_quant" "-t" "2" "-m" "t2g_3col.tsv" "-r" "cr-like"
  2025-03-01T01:54:59.014640Z  INFO simpleaf::utils::prog_utils: command returned successfully (exit status: 0)
  2025-03-01T01:54:59.014892Z  WARN af_anndata: Could not find the `gene_id_to_name` file, so only gene IDs and not symbols will be present in `var`
  2025-03-01T01:54:59.016695Z  INFO af_anndata: USA mode : true

Command error:
  found `piscem` in the PATH at /usr/local/bin/piscem
  found `salmon` in the PATH at /usr/local/bin/salmon
  found `alevin-fry` in the PATH at /usr/local/bin/alevin-fry
  2025-03-01T01:54:56.659805Z  INFO simpleaf::utils::prog_utils: Could not find macs3 executable, peak calling cannot be peformed by simpleaf
  2025-03-01T01:54:56.737143Z  INFO simpleaf::simpleaf_commands::quant: found file compressed using Gzip
  2025-03-01T01:54:56.737276Z  INFO simpleaf::simpleaf_commands::quant: piscem map-sc cmd : /usr/local/bin/piscem map-sc --index index/piscem_idx --threads 2 -o simpleaf_quant/af_map --max-ec-card 4096 --skipping-strategy permissive --max-hit-occ 256 --max-hit-occ-recover 1024 --max-read-occ 2500 -1 Sample_Y_S1_L001_R1_001.fastq.gz,Sample_Y_S1_L002_R1_001.fastq.gz -2 Sample_Y_S1_L001_R2_001.fastq.gz,Sample_Y_S1_L002_R2_001.fastq.gz --geometry chromium_v2
  2025-03-01T01:54:58.738656Z  INFO simpleaf::utils::prog_utils: command returned successfully (exit status: 0)
  2025-03-01T01:54:58.738690Z  INFO simpleaf::simpleaf_commands::quant: alevin-fry generate-permit-list cmd : /usr/local/bin/alevin-fry generate-permit-list -i simpleaf_quant/af_map -d fw --unfiltered-pl 10x_V2_barcode_whitelist.txt.gz --min-reads 10 -o simpleaf_quant/af_quant
  2025-03-01T01:54:58.997685Z  INFO simpleaf::utils::prog_utils: command returned successfully (exit status: 0)
  2025-03-01T01:54:58.997766Z  INFO simpleaf::simpleaf_commands::quant: alevin-fry collate cmd : /usr/local/bin/alevin-fry collate -i simpleaf_quant/af_quant -r simpleaf_quant/af_map -t 2
  2025-03-01T01:54:59.006392Z  INFO simpleaf::utils::prog_utils: command returned successfully (exit status: 0)
  2025-03-01T01:54:59.006608Z  INFO simpleaf::simpleaf_commands::quant: cmd : "/usr/local/bin/alevin-fry" "quant" "-i" "simpleaf_quant/af_quant" "-o" "simpleaf_quant/af_quant" "-t" "2" "-m" "t2g_3col.tsv" "-r" "cr-like"
  2025-03-01T01:54:59.014640Z  INFO simpleaf::utils::prog_utils: command returned successfully (exit status: 0)
  2025-03-01T01:54:59.014892Z  WARN af_anndata: Could not find the `gene_id_to_name` file, so only gene IDs and not symbols will be present in `var`
  2025-03-01T01:54:59.016695Z  INFO af_anndata: USA mode : true
  Error: no data: empty CSV

Work dir:
  /home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/bd38a769ad3f15ed40dc61fc091ff019/work/83/7b084d23aa21abb488592463d4f46b

Container:
  quay.io/biocontainers/simpleaf:0.19.2--ha6fb395_0

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

 -- Check '/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/bd38a769ad3f15ed40dc61fc091ff019/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/bd38a769ad3f15ed40dc61fc091ff019/meta/nextflow.log' file for details
Nextflow stderr:
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