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pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
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Reduce verbosity of refgenie tag plugin? #529

Open nsheff opened 1 month ago

nsheff commented 1 month ago

when running vanilla pepatac, I got this message.

Is there a way to streamline this? Like, maybe aggregate these and then print one list instead of duplicating the message?

## [1 of 16] sample: 1865; pipeline: PEPATAC
Calling pre-submit function: refgenconf.looper_refgenie_populate
Refgenie asset (demo1/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (demo2/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (dm6/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (dm6/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18/cellranger_reference) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18/fasta_txome) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18/gencode_gtf) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18_cdna/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18_cdna/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18_cdna/kallisto_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg18_cdna/salmon_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/cellranger_reference) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/dbsnp) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/ensembl_gtf) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/ensembl_rb) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/fasta_txome) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/feat_annotation) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/gencode_gtf) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/refgene_anno) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/salmon_partial_sa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/salmon_sa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19_cdna/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19_cdna/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19_cdna/kallisto_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg19_cdna/salmon_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/blacklist) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/cellranger_reference) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/dbnsfp) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/dbsnp) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/ensembl_gtf) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/ensembl_rb) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/epilog_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/fasta_txome) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/feat_annotation) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/gencode_gtf) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/refgene_anno) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/salmon_partial_sa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/salmon_sa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/split_fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_cdna/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_cdna/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_cdna/kallisto_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_cdna/salmon_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_chr22/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_chr22/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_chr22/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_chr22/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_chr22/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_chr22/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_chr22/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_chr22/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_chr22/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_noalt_decoy/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_noalt_decoy/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_noalt_decoy/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_noalt_decoy/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_noalt_decoy/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_noalt_decoy/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_noalt_decoy/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_noalt_decoy/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hg38_noalt_decoy/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hs38d1/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hs38d1/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hs38d1/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hs38d1/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hs38d1/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hs38d1/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hs38d1/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hs38d1/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (hs38d1/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alphasat/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alphasat/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alphasat/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alphasat/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alphasat/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alphasat/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alphasat/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alphasat/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alphasat/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alu/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alu/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alu/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alu/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alu/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alu/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alu/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_alu/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_rDNA/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_rDNA/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_rDNA/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_rDNA/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_rDNA/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_rDNA/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_rDNA/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_rDNA/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_rDNA/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_repeats/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_repeats/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_repeats/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_repeats/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_repeats/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_repeats/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_repeats/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_repeats/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (human_repeats/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (meth_spikein_k12/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (meth_spikein_k1_k3/epilog_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (meth_spikein_k1_k3/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/cellranger_reference) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/ensembl_gtf) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/ensembl_rb) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/fasta_txome) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/feat_annotation) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/gencode_gtf) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/refgene_anno) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/salmon_partial_sa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/salmon_sa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10_cdna/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10_cdna/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10_cdna/kallisto_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mm10_cdna/salmon_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mouse_chrM2x/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mouse_chrM2x/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mouse_chrM2x/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mouse_chrM2x/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mouse_chrM2x/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mouse_chrM2x/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mouse_chrM2x/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mouse_chrM2x/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (mouse_chrM2x/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rCRSd/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rCRSd/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rCRSd/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rCRSd/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rCRSd/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rCRSd/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rCRSd/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (renin_transgenes/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/bismark_bt1_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/bismark_bt2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/bwa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/ensembl_gtf) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/fasta_txome) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/refgene_anno) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/salmon_partial_sa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/salmon_sa_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/star_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/suffixerator_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6/tallymer_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6_cdna/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6_cdna/hisat2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6_cdna/kallisto_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (rn6_cdna/salmon_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (t7/bowtie2_index) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default
Refgenie asset (t7/fasta) tag not specified in `refgenie.tag_overrides` section. Using the default tag: default

Not sure if this should happen here or with refgenie

nsheff commented 1 month ago

Yeah, this is making looper basically unusable in my hands. I cannot see what's actually going on because there are 100 messages spitting out, for each sample.

nsheff commented 1 month ago

Here's the culprit: https://github.com/refgenie/refgenconf/blob/727fe1f219780b46fe3743a906dcd6238f1734f6/refgenconf/populator.py#L61