chore: apply suggestions from code review

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Validate Inputs on: push 1

validate_inputs

Python CI on: push 2

python-format

python-lint

Workflows Sprocket Lint on: push 1

sprocket_lint

R CI on: push 2

style

lint

Build and Test on: push 56

call-build / list-images

call-build / build-images (docker/pandas)

call-build / build-images (docker/bwa)

call-build / build-images (docker/util)

call-build / build-images (docker/umap)

call-build / build-images (docker/python-plotting)

call-build / build-images (docker/minfi)

call-test / list-files

call-test / sprocket_test (./workflows/general/bam-to-fastqs.wdl, sprocket)

call-test / sprocket_test (./workflows/general/alignment-post.wdl, sprocket)

call-test / sprocket_test (./workflows/general/samtools-merge.wdl, sprocket)

call-test / sprocket_test (./workflows/qc/quality-check-standard.wdl, sprocket)

call-test / sprocket_test (./workflows/qc/markdups-post.wdl, sprocket)

call-test / sprocket_test (./workflows/chipseq/chipseq-standard.wdl, sprocket)

call-test / sprocket_test (./workflows/dnaseq/dnaseq-standard-fastq.wdl, sprocket)

call-test / sprocket_test (./workflows/dnaseq/dnaseq-core.wdl, sprocket)

call-test / sprocket_test (./workflows/dnaseq/dnaseq-standard.wdl, sprocket)

call-test / sprocket_test (./workflows/rnaseq/rnaseq-core.wdl, sprocket)

call-test / sprocket_test (./workflows/rnaseq/rnaseq-standard.wdl, sprocket)

call-test / sprocket_test (./workflows/rnaseq/rnaseq-standard-fastq.wdl, sprocket)

call-test / sprocket_test (./workflows/rnaseq/rnaseq-variant-calling.wdl, sprocket)

call-test / sprocket_test (./workflows/methylation/methylation-preprocess.wdl, sprocket)

call-test / sprocket_test (./workflows/methylation/methylation-cohort.wdl, sprocket)

call-test / sprocket_test (./workflows/methylation/methylation-standard.wdl, sprocket)

call-test / sprocket_test (./workflows/reference/gatk-reference.wdl, sprocket)

call-test / sprocket_test (./workflows/reference/star-db-build.wdl, sprocket)

call-test / sprocket_test (./workflows/reference/bwa-db-build.wdl, sprocket)

call-test / sprocket_test (./workflows/reference/qc-reference.wdl, sprocket)

call-test / sprocket_test (./data_structures/flag_filter.wdl, sprocket)

call-test / sprocket_test (./data_structures/read_group.wdl, sprocket)

call-test / sprocket_test (./tools/deeptools.wdl, sprocket)

call-test / sprocket_test (./tools/multiqc.wdl, sprocket)

call-test / sprocket_test (./tools/librarian.wdl, sprocket)

call-test / sprocket_test (./tools/fastqc.wdl, sprocket)

call-test / sprocket_test (./tools/ngsderive.wdl, sprocket)

call-test / sprocket_test (./tools/kraken2.wdl, sprocket)

call-test / sprocket_test (./tools/fq.wdl, sprocket)

call-test / sprocket_test (./tools/mosdepth.wdl, sprocket)

call-test / sprocket_test (./tools/star.wdl, sprocket)

call-test / sprocket_test (./tools/md5sum.wdl, sprocket)

call-test / sprocket_test (./tools/htseq.wdl, sprocket)

call-test / sprocket_test (./tools/gatk4.wdl, sprocket)

call-test / sprocket_test (./tools/arriba.wdl, sprocket)

call-test / sprocket_test (./tools/picard.wdl, sprocket)

call-test / sprocket_test (./tools/samtools.wdl, sprocket)

call-test / sprocket_test (./tools/qualimap.wdl, sprocket)

call-test / sprocket_test (./tools/util.wdl, sprocket)

call-test / sprocket_test (./tools/sambamba.wdl, sprocket)

call-test / sprocket_test (./tools/fastp.wdl, sprocket)

call-test / sprocket_test (./tools/bwa.wdl, sprocket)

Workflows Pull Check on: pull_request 2

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