From 8f5b9cbc757b0352a143b3a0a8f086a64aade1b2 Mon Sep 17 00:00:00 2001
From: daniel <d4straub@gmail.com>
Date: Wed, 16 Aug 2023 14:49:45 +0200
Subject: [PATCH] update file names

---
 tests/pipeline/single.nf.test | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/pipeline/single.nf.test b/tests/pipeline/single.nf.test
index 02d54e9e..11bb9156 100644
--- a/tests/pipeline/single.nf.test
+++ b/tests/pipeline/single.nf.test
@@ -24,10 +24,10 @@ nextflow_pipeline {
                                 path("$outputDir/barrnap/rrna.mito.gff")).match("barrnap") },
                 { assert new File("$outputDir/barrnap/summary.tsv").exists() },
                 { assert snapshot(path("$outputDir/cutadapt/cutadapt_summary.tsv")).match("cutadapt") },
-                { assert new File("$outputDir/cutadapt/1a_S103_L001_R1_001.trimmed.cutadapt.log").exists() },
-                { assert new File("$outputDir/cutadapt/1_S103_L001_R1_001.trimmed.cutadapt.log").exists() },
-                { assert new File("$outputDir/cutadapt/2a_S115_L001_R1_001.trimmed.cutadapt.log").exists() },
-                { assert new File("$outputDir/cutadapt/2_S115_L001_R1_001.trimmed.cutadapt.log").exists() },
+                { assert new File("$outputDir/cutadapt/sampleID_1a.trimmed.cutadapt.log").exists() },
+                { assert new File("$outputDir/cutadapt/sampleID_1.trimmed.cutadapt.log").exists() },
+                { assert new File("$outputDir/cutadapt/sampleID_2a.trimmed.cutadapt.log").exists() },
+                { assert new File("$outputDir/cutadapt/sampleID_2.trimmed.cutadapt.log").exists() },
                 { assert new File("$outputDir/cutadapt/assignTaxonomy.cutadapt.log").exists() },
                 { assert snapshot(path("$outputDir/dada2/ASV_seqs.fasta"),
                                 path("$outputDir/dada2/ASV_table.tsv"),
@@ -37,11 +37,11 @@ nextflow_pipeline {
                                 path("$outputDir/dada2/DADA2_table.tsv")).match("dada2") },
                 { assert new File("$outputDir/dada2/ASV_tax.rdp_18.tsv").exists() },
                 { assert new File("$outputDir/dada2/ASV_tax_species.rdp_18.tsv").exists() },
-                { assert new File("$outputDir/fastqc/1a_S103_L001_R1_001_fastqc.html").exists() },
-                { assert new File("$outputDir/fastqc/1_S103_L001_R1_001_fastqc.html").exists() },
-                { assert new File("$outputDir/fastqc/2a_S115_L001_R1_001_fastqc.html").exists() },
-                { assert new File("$outputDir/fastqc/2_S115_L001_R1_001_fastqc.html").exists() },
-                { assert snapshot(path("$outputDir/input/Samplesheet_single_end.tsv")).match("input") },
+                { assert new File("$outputDir/fastqc/sampleID_1a_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/sampleID_1_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/sampleID_2a_fastqc.html").exists() },
+                { assert new File("$outputDir/fastqc/sampleID_2_fastqc.html").exists() },
+                { assert snapshot(path("$outputDir/input/Samplesheet.tsv")).match("input") },
                 { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
                                 path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
                                 path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },