Fix read indexing in AdapterRemoval module (#1051)

* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pydamage/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* split tests

* export env variable

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* answer PR comments and switch to bgzip

* fix read index

* update test.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

modules/adapterremoval/main.nf

@@ -49,7 +49,7 @@ process ADAPTERREMOVAL {
         """
         AdapterRemoval  \\
             --file1 ${reads[0]} \\
-            --file2 ${reads[0]} \\
+            --file2 ${reads[1]} \\
             $options.args \\
             --basename $prefix \\
             --threads $task.cpus \\
@@ -68,7 +68,7 @@ process ADAPTERREMOVAL {
         """
         AdapterRemoval  \\
             --file1 ${reads[0]} \\
-            --file2 ${reads[0]} \\
+            --file2 ${reads[1]} \\
             --collapse \\
             $options.args \\
             --basename $prefix \\

tests/modules/adapterremoval/test.yml

@@ -13,12 +13,12 @@
   tags:
     - adapterremoval
   files:
-    - path: output/adapterremoval/test.pair2.trimmed.fastq.gz
-      md5sum: f076a9f666235e01a3281f8c46c9d010
     - path: output/adapterremoval/test.log
-      md5sum: bea86105aff4d27fe29c83e24498fefa
+      md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
     - path: output/adapterremoval/test.pair1.trimmed.fastq.gz
-      md5sum: f076a9f666235e01a3281f8c46c9d010
+      md5sum: 294a6277f0139bd597e57c6fa31f39c7
+    - path: output/adapterremoval/test.pair2.trimmed.fastq.gz
+      md5sum: de7b38e2c881bced8671acb1ab452d78
 
 - name: adapterremoval test_adapterremoval_paired_end_collapse
   command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
@@ -26,6 +26,6 @@
     - adapterremoval
   files:
     - path: output/adapterremoval/test.log
-      md5sum: 97cb97b3d03123ac88430768b2e36c59
+      md5sum: 7f0b2328152226e46101a535cce718b3
     - path: output/adapterremoval/test.merged.fastq.gz
-      md5sum: 50a4f9fdac6a24e211eb4dcf9f292bef
+      md5sum: 07a8f725bfd3ecbeabdc41b32d898dee