Skip fastq>a conversion

CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [unreleased]
+### Changed
+- Skip unnecessary conversion to fasta from fastq.
+
 ## [v0.1.4]
 ### Changed
 - Args parser for fastqingress

nextflow_schema.json

@@ -15,7 +15,7 @@
                 "out_dir": {
                     "type": "string",
                     "default": "output",
-                    "format": "path",
+                    "format": "directory-path",
                     "description": "Directory for output of all user-facing files."
                 },
                 "fastq": {

reference_assembly.nf

@@ -20,8 +20,7 @@ process map_reads{
         RightShift: ${params.poly_context}, RegexEnd: "[Aa]{${params.max_poly_run},}",
         Stranded: True,Invert: True, Tsv: "internal_priming_fail.tsv"} """
     """
-    seqkit fq2fa ${fastq_reads} -o "reads.fa";
-    minimap2 -t ${params.threads} -ax splice ${params.minimap2_opts} ${index} "reads.fa"\
+    minimap2 -t ${params.threads} -ax splice ${params.minimap2_opts} ${index} ${fastq_reads}\
         | samtools view -q ${params.minimum_mapping_quality} -F 2304 -Sb -\
         | seqkit bam -j ${params.threads} -x -T '${ContextFilter}' -\
         | samtools sort -@ ${params.threads} -o "${sample_id}_reads_aln_sorted.bam" - ;