From 1fbe69cfcc13ab98ee20c7eb6fdb3aaac420a9d0 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
Date: Fri, 10 Jun 2022 11:46:23 +0200
Subject: [PATCH] Updated and fixed tests

---
 tests/modules/cellranger/count/test.yml | 54 +++++++++++++++++++++++--
 tests/modules/cellranger/mkgtf/test.yml |  4 +-
 tests/modules/cellranger/mkref/test.yml |  4 +-
 3 files changed, 55 insertions(+), 7 deletions(-)

diff --git a/tests/modules/cellranger/count/test.yml b/tests/modules/cellranger/count/test.yml
index e29baaf0..2f49daf5 100644
--- a/tests/modules/cellranger/count/test.yml
+++ b/tests/modules/cellranger/count/test.yml
@@ -1,10 +1,53 @@
 - name: cellranger count test_cellranger_count
-  command: nextflow run tests/modules/cellranger/count -entry test_cellranger_count -c tests/config/nextflow.config -c tests/modules/cellranger/count/nextflow.config
+  command: nextflow run ./tests/modules/cellranger/count -entry test_cellranger_count -c ./tests/config/nextflow.config  -c ./tests/modules/cellranger/count/nextflow.config
   tags:
-    - cellranger
     - cellranger/count
+    - cellranger
   files:
+    - path: output/cellranger/genome.filtered.gtf
+      md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
+    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
+      md5sum: f315020d899597c1b57e5fe9f60f4c3e
+    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa.fai
+      md5sum: 3520cd30e1b100e55f578db9c855f685
+    - path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
+      md5sum: d1e05cd46684fa26d852b6bc9f05e31f
+    - path: output/cellranger/homo_sapiens_chr22_reference/reference.json
+      md5sum: 8405fd7f527a944eafb9c2909045840b
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
+      md5sum: 897cec2d191945335f8b320438bd9135
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/SA
+      md5sum: 7961129ac5d0e1706105be1d31c6b30c
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/SAindex
+      md5sum: dcceb480b30cda93fb8c63ddc339093b
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrLength.txt
+      md5sum: c81f40f27e72606d7d07097c1d56a5b5
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrName.txt
+      md5sum: 5ae68a67b70976ee95342a7451cb5af1
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrNameLength.txt
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrStart.txt
+      md5sum: bc73df776dd3d5bb9cfcbcba60880519
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonGeTrInfo.tab
+      md5sum: 9129691eeb4ed0d02b17be879fa3edb0
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonInfo.tab
+      md5sum: 209b82f0683efd03e17d2c729676554f
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/geneInfo.tab
+      md5sum: 02a8f4575bdfcd4a42b4d8d07f2e9369
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/genomeParameters.txt
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
+      md5sum: 1082ab459363b3f2f7aabcef0979c1ed
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab
+      md5sum: cedcb5f4e7d97bc548cd5daa022e092c
     - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5
+      md5sum: f8b6b7cc8248151a98c46d4ebec450c6
+    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
+    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/features.tsv.gz
+    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/matrix.mtx.gz
     - path: output/cellranger/sample-123/outs/metrics_summary.csv
       md5sum: 707df0f101d479d93f412ca74f9c4131
     - path: output/cellranger/sample-123/outs/molecule_info.h5
@@ -13,7 +56,12 @@
       md5sum: 15441da9cfceea0bb48c8b66b1b860df
     - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai
       md5sum: 7c3d49c77016a09535aff61a027f750c
-    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix
     - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5
       md5sum: a5290f3e300a4070f3d68a0c2e215f54
+    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/barcodes.tsv.gz
+      md5sum: 5cc39ef0c7ac85f2b758b164aabf9157
+    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/features.tsv.gz
+      md5sum: 07d497c7ce3e22f374af7b2cf9b97d72
+    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/matrix.mtx.gz
+      md5sum: bdce94a51f16e22d40301724080b76ee
     - path: output/cellranger/sample-123/outs/web_summary.html
diff --git a/tests/modules/cellranger/mkgtf/test.yml b/tests/modules/cellranger/mkgtf/test.yml
index 2130afd2..59eb9072 100644
--- a/tests/modules/cellranger/mkgtf/test.yml
+++ b/tests/modules/cellranger/mkgtf/test.yml
@@ -1,8 +1,8 @@
 - name: cellranger mkgtf test_cellranger_mkgtf
-  command: nextflow run tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c tests/config/nextflow.config -c tests/modules/cellranger/mkgtf/nextflow.config
+  command: nextflow run ./tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c ./tests/config/nextflow.config  -c ./tests/modules/cellranger/mkgtf/nextflow.config
   tags:
-    - cellranger
     - cellranger/mkgtf
+    - cellranger
   files:
     - path: output/cellranger/genome.filtered.gtf
       md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
diff --git a/tests/modules/cellranger/mkref/test.yml b/tests/modules/cellranger/mkref/test.yml
index 3f63b59c..83ec5f95 100644
--- a/tests/modules/cellranger/mkref/test.yml
+++ b/tests/modules/cellranger/mkref/test.yml
@@ -1,8 +1,8 @@
 - name: cellranger mkref test_cellranger_mkref
-  command: nextflow run ./tests/modules/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/mkref/nextflow.config
+  command: nextflow run ./tests/modules/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config  -c ./tests/modules/cellranger/mkref/nextflow.config
   tags:
-    - cellranger
     - cellranger/mkref
+    - cellranger
   files:
     - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
       md5sum: f315020d899597c1b57e5fe9f60f4c3e