From fd106a20a95cae7e096a200e6158aa70971b65cd Mon Sep 17 00:00:00 2001
From: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Date: Mon, 15 Jul 2024 15:07:48 +0200
Subject: [PATCH] Apply suggestions from code review

Co-authored-by: Till E. <64961761+tillenglert@users.noreply.github.com>
---
 workflows/ampliseq.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
index 5105b545..f0073841 100644
--- a/workflows/ampliseq.nf
+++ b/workflows/ampliseq.nf
@@ -272,9 +272,9 @@ workflow AMPLISEQ {
             .map{ meta, readfw, readrv ->
                 meta.single_end = single_end.toBoolean()
                 def reads = single_end ? readfw : [readfw,readrv]
-                if ( !meta.single_end && !readrv ) { error("Entry `reverseReads` is missing in $params.input for $meta.sample, either correct the samplesheet or use `--single_end`, `--pacbio`, or `--iontorrent`") } // make sure that reverse reads are present when single_end isnt specified
-                if ( !meta.single_end && ( readfw.getSimpleName() == meta.sample || readrv.getSimpleName() == meta.sample ) ) { error("Entry `sampleID` cannot be identical to simple name of `forwardReads` or `reverseReads`, please change `sampleID` in $params.input for sample $meta.sample") } // sample name and any file name without extensions arent identical, because rename_raw_data_files.nf would forward 3 files (2 renamed +1 input) instead of 2 in that case
-                if ( meta.single_end && ( readfw.getSimpleName() == meta.sample+"_1" || readfw.getSimpleName() == meta.sample+"_2" ) ) { error("Entry `sampleID`+ `_1` or `_2` cannot be identical to simple name of `forwardReads`, please change `sampleID` in $params.input for sample $meta.sample") } // sample name and file name without extensions arent identical, because rename_raw_data_files.nf would forward 2 files (1 renamed +1 input) instead of 1 in that case
+                if ( !meta.single_end && !readrv ) { error("Entry `reverseReads` is missing in $params.input for $meta.sample, either correct the samplesheet or use `--single_end`, `--pacbio`, or `--iontorrent`") } // make sure that reverse reads are present when single_end isn't specified
+                if ( !meta.single_end && ( readfw.getSimpleName() == meta.sample || readrv.getSimpleName() == meta.sample ) ) { error("Entry `sampleID` cannot be identical to simple name of `forwardReads` or `reverseReads`, please change `sampleID` in $params.input for sample $meta.sample") } // sample name and any file name without extensions aren't identical, because rename_raw_data_files.nf would forward 3 files (2 renamed +1 input) instead of 2 in that case
+                if ( meta.single_end && ( readfw.getSimpleName() == meta.sample+"_1" || readfw.getSimpleName() == meta.sample+"_2" ) ) { error("Entry `sampleID`+ `_1` or `_2` cannot be identical to simple name of `forwardReads`, please change `sampleID` in $params.input for sample $meta.sample") } // sample name and file name without extensions aren't identical, because rename_raw_data_files.nf would forward 2 files (1 renamed +1 input) instead of 1 in that case
                 return [meta, reads] }
     } else if ( params.input_fasta ) {
         ch_input_fasta = Channel.fromPath(params.input_fasta, checkIfExists: true)