RuleException in rule collect_cohort_mafs when using --pairs

[kelly-sovacool]

This does not happen without the --pairs option.

./bin/xavier run \
--input ./tests/data/*R?*.fastq.gz  \
--output /data/$USER/xavier_hg38_pairs \
--genome hg38 \
--mode local \
--runmode dryrun \
--pairs ./tests/data/pairs.tsv \
> dryrun.out

dryrun.out

Thank you for running XAVIER on BIOWULF
--Dry-Run
Command '['snakemake', '-npr', '--rerun-incomplete', '-s', 'workflow/Snakefile', '--use-singularity', '--cores', '1', '--configfile=config.json']' returned non-zero exit status 1. b'Config file config.json is extended by additional config specified via the command line.
FQS_FOUND: WES_NC_T_1_sub.R1.fastq.gz, WES_NC_T_1_sub.R2.fastq.gz, WES_NC_N_1_sub.R2.fastq.gz, WES_NC_N_1_sub.R1.fastq.gz
NAME_SYMLINKS: /gpfs/gsfs12/users/sovacoolkl/xavier_hg38_pairs/input_files/fastq/WES_NC_T_1_sub.R1.fastq.gz, /gpfs/gsfs12/users/sovacoolkl/xavier_hg38_pairs/input_files/fastq/WES_NC_T_1_sub.R2.fastq.gz, /gpfs/gsfs12/users/sovacoolkl/xavier_hg38_pairs/input_files/fastq/WES_NC_N_1_sub.R2.fastq.gz, /gpfs/gsfs12/users/sovacoolkl/xavier_hg38_pairs/input_files/fastq/WES_NC_N_1_sub.R1.fastq.gz
SAMPLES: WES_NC_N_1_sub, WES_NC_T_1_sub
Building DAG of jobs...
Singularity image docker://nciccbr/ccbr_fastqc_0.11.9:v1.1 will be pulled.
Singularity image docker://nciccbr/ccbr_qualimap:v0.0.1 will be pulled.
Singularity image docker://nciccbr/ccbr_fastq_screen_0.13.0:v2.0 will be pulled.
Singularity image docker://nciccbr/ccbr_python:v0.0.1 will be pulled.
Singularity image docker://nciccbr/ccbr_multiqc_1.15:v2 will be pulled.
Singularity image docker://nciccbr/ccbr_wes_base:1.1.1 will be pulled.
Singularity image docker://nciccbr/ccbr_kraken_v2.1.1:v0.0.1 will be pulled.
Singularity image docker://nciccbr/ccbr_picard:v0.0.1 will be pulled.
Job stats:
job                          count
-------------------------  -------
Gatk_SelectVariants              2
Gatk_Variantfilter               1
all                              1
bam2fastq                        2
bam_check                        2
bcftools_stats                   2
bwa_mem                          2
collect_cohort_mafs              5
collectvariantcallmetrics        1
fastq_screen                     2
fastqc_bam                       2
fc_lane                          2
gatk_recal                       2
gatk_varianteval                 2
genotype                        25
germline_merge_chrom             1
haplotypecaller                 50
kraken                           2
mergegvcfs                      25
multiqc                          1
qualimap_bamqc                   2
raw_index                        2
reformat_targets_bed             1
samtools_flagstats               2
snpeff                           2
somalier_analysis                1
somalier_extract                 2
trimmomatic                      2
vcftools                         1
total                          147


[Wed Jan 14 10:33:50 2026]
localrule collect_cohort_mafs:
    output: /gpfs/gsfs12/users/sovacoolkl/xavier_hg38_pairs/somatic_tumor_only/SNP_Indels/merged_somatic_variants/cohort_summary/all_somatic_variants.maf
    jobid: 121
    reason: Missing output files: /gpfs/gsfs12/users/sovacoolkl/xavier_hg38_pairs/somatic_tumor_only/SNP_Indels/merged_somatic_variants/cohort_summary/all_somatic_variants.maf
    wildcards: vc_outdir=merged_somatic_variants
    resources: tmpdir=/tmp

RuleException in rule collect_cohort_mafs in file /gpfs/gsfs12/users/sovacoolkl/xavier_hg38_pairs/workflow/rules/somatic_snps.common.smk, line 220:
IndexError: list index out of range, when formatting the following:

    echo "Combining MAFs..."
    head -2 {input.mafs[0]} > {output.maf}
    awk \'FNR>2 {{print}}\' {input.mafs} >> {output.maf}
    
'

[samarth8392]

it was an issue with the difference in sample names in the test/data folder
the files are labeled

 $ ls XAVIER/tests/data/*.gz
WES_NC_N_1_sub.R1.fastq.gz  WES_NC_N_1_sub.R2.fastq.gz  WES_NC_T_1_sub.R1.fastq.gz  WES_NC_T_1_sub.R2.fastq.gz

but the pairs were labelled

Normal  Tumor
  WES_NC_N_1_0.25 WES_NC_T_1_0.25

Fixed in #174