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Running with ITS region set to ITS1_5.8S_ITS2 fails on documentation step #13

@hadawson

Description

@hadawson

Runs made with the its_region parameter set to ITS1_5.8S_ITS2 appears to cause issues during the documentation process in document_s1.R. As an example, this configuration, where $ITSX_REGION is set to ITS1_5.8S_ITS2:

nextflow run vmikk/NextITS -r main \
	-profile     docker \
	-resume \
	--step       "Step1" \
	--input      "$BASEDIR"/Input/"$1"/*.fastq \
	--barcodes   "$BASEDIR"/Input/"$1"/*.fasta \
	--lima_barcodetype $LIMA_BARCODETYPE \
	--lima_minlen $LIMA_MINLEN \
	--primer_forward "$PRIMER_FORWARD" \
	--primer_reverse "$PRIMER_REVERSE" \
	--its_region "$ITS_REGION" \
	--ITSx_tax "$ITSX_TAX" \
	--chimera_db "$BASEDIR"/Utility/UN95_chimera.udb \
	--outdir     "$BASEDIR"/Step1_Results/"$1" \
	-work-dir    "$BASEDIR"/Step1_WorkDirs/"$1"

Fails the run with this error on the last step:

Error in emit_assemble_its(params, versions) : 
    could not find function "emit_assemble_its"

Meanwhile, running the same setup with its_region set to full completes successfully, since it's no longer calling emit_assemble_its anywhere. As can be seen above, this is using the standard NextITS and Docker container versions, so hopefully it is reproducible with relative ease.

As of right now this is a complete blocker - is there perhaps also a way to force skip the documentation step as a temporary workaround?

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