refactor: change oligomap output extension (#133)

* refactor: change oligomap output extension * test: update expected output
zavolanlab · Jan 30, 2024 · e1e19d7 · e1e19d7
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commit e1e19d7
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diff --git a/test/expected_output.md5 b/test/expected_output.md5
@@ -6,28 +6,27 @@ cc01c7884838a597c587437cb0acf64e  results/test_lib/alignments_intersecting_mirna
 b1eb81426f890d671bba8c8a815edc1e  results/test_lib/alignments_intersecting_primir.sam
 eec9be6cda61d2728290c92c1209f455  results/intermediates/TABLES/mirna_counts_test_lib
 a844e3a29159e36e2f17a0646d1e8c5f  results/intermediates/TABLES/pri-mir_counts_test_lib
-36f7d024fe6ddfd3e788aebf61c61061  results/intermediates/test_lib/oligomap_genome_sorted.fasta
 48e605df55bf2dd37ea5a5a74eb5872a  results/intermediates/test_lib/mappings_all.sam
-d41d8cd98f00b204e9800998ecf8427e  results/intermediates/test_lib/oligomap_transcriptome_mappings.fasta
 e9aac4afeb2053385d60f5e4b07a9774  results/intermediates/test_lib/mappings_all_removed_inferiors.sam
 9ebcb4ac877f37921b88ceca3ff03b62  results/intermediates/test_lib/alignments_intersecting_primir.bam
-defdc8c46e1d73692edde0e0278f2d5e  results/intermediates/test_lib/oligomap_genome_mappings.fasta
 e632f8984d423d46bbb377ec75468521  results/intermediates/test_lib/segemehl_transcriptome_mappings.sam
 e632f8984d423d46bbb377ec75468521  results/intermediates/test_lib/transcriptome_mappings_filtered_nh.sam
 3344bbeb9fe01f07c04831e5b4a795ba  results/intermediates/test_lib/alignments_all.bam
 a124a5afdb5f7bfbcc5683260556c9c4  results/intermediates/test_lib/mappings_all_no_header.sam
 d62630102c33d43d593af14c2a642839  results/intermediates/test_lib/alignments_all.sam
+defdc8c46e1d73692edde0e0278f2d5e  results/intermediates/test_lib/oligomap_genome_mappings.oligomap
 81103749d61bc55ee2cfc84ca1527456  results/intermediates/test_lib/alignments_intersecting_mirna_tag.sam
-d41d8cd98f00b204e9800998ecf8427e  results/intermediates/test_lib/oligomap_transcriptome_sorted.fasta
 76643f87bb2e2bff77d1b1223d7720b5  results/intermediates/test_lib/segemehl_genome_mappings.sam
 d41d8cd98f00b204e9800998ecf8427e  results/intermediates/test_lib/transcriptome_mappings_to_genome.sam
+d41d8cd98f00b204e9800998ecf8427e  results/intermediates/test_lib/oligomap_transcriptome_mappings.oligomap
 63a32839360a985b68e0685aafad5c54  results/intermediates/test_lib/fa/reads.fa
 0a0d69662aa8190abdcd8f395802ab00  results/intermediates/test_lib/alignments_intersecting_mirna_uncollapsed.sam
 edcb854702519c0002d8ce89a21e54ef  results/intermediates/test_lib/reads_formatted.fasta
 1a547487b8e92ad85bb26ff9b1db1f93  results/intermediates/test_lib/intersected_extended_mirna.bed
 a287ffc43b6afbdde3e9905bc27c28a5  results/intermediates/test_lib/alignments_all_sorted_test_lib.bam
 ec0e9bcc8ea857da897035c8fca4078f  results/intermediates/test_lib/reads_trimmed_adapters.fasta
 37c74848cbbba56e29e240cc078f5249  results/intermediates/test_lib/alignments_intersecting_mirna_uncollapsed.bam
+36f7d024fe6ddfd3e788aebf61c61061  results/intermediates/test_lib/oligomap_genome_sorted.oligomap
 1f1b873d05ec14ef9b16376a1c98315b  results/intermediates/test_lib/genome_mappings.sam
 f5cb65466d328036a15b66cfbd4d8419  results/intermediates/test_lib/oligomap_genome_report.txt
 6cbdb9299e09b3e39b79a50db69226b5  results/intermediates/test_lib/transcriptome_mappings_no_header.sam
@@ -43,6 +42,7 @@ a124a5afdb5f7bfbcc5683260556c9c4  results/intermediates/test_lib/genome_mappings
 f68693cfaa1e6ea78e1a5562ade6d9ed  results/intermediates/test_lib/intersected_extended_primir.bed
 c2a5770a755ada66ef63d96eec4afb00  results/intermediates/test_lib/reads_filtered_for_oligomap.fasta
 fe5388094985e9604a302d39d2abc82c  results/intermediates/test_lib/oligomap_transcriptome_report.txt
+d41d8cd98f00b204e9800998ecf8427e  results/intermediates/test_lib/oligomap_transcriptome_sorted.oligomap
 96a178aabc41d3020992efd6acbecb5a  results/intermediates/genome_processed.fa.bz
 d34fc868b861b1bc46db07a397dc0f10  results/intermediates/genome_processed.fa.bz.fai
 be7a0d92e57480190de57eb30baffa36  results/intermediates/extended_mirna_annotation_6_nt.gff3

diff --git a/workflow/rules/map.smk b/workflow/rules/map.smk
@@ -343,7 +343,7 @@ rule map_genome_oligomap:
         reads=INTERMEDIATES_DIR / "{sample}" / "reads_filtered_for_oligomap.fasta",
         target=INTERMEDIATES_DIR / "genome_processed.fa",
     output:
-        gmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_mappings.fasta",
+        gmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_mappings.oligomap",
         report=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_report.txt",
     params:
         cluster_log=CLUSTER_LOG / "map_genome_oligomap_{sample}.log",
@@ -373,10 +373,10 @@ rule map_genome_oligomap:
 
 rule sort_genome_oligomap:
     input:
-        tmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_mappings.fasta",
+        tmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_mappings.oligomap",
         script=SCRIPTS_DIR / "blocksort.sh",
     output:
-        sort=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_sorted.fasta",
+        sort=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_sorted.oligomap",
     params:
         cluster_log=CLUSTER_LOG / "sort_genome_oligomap_{sample}.log",
     log:
@@ -401,7 +401,7 @@ rule sort_genome_oligomap:
 
 rule convert_genome_to_sam_oligomap:
     input:
-        sort=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_sorted.fasta",
+        sort=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_sorted.oligomap",
         script=SCRIPTS_DIR / "oligomap_output_to_sam_nh_filtered.py",
     output:
         gmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_genome_mappings.sam",
@@ -434,7 +434,7 @@ rule map_transcriptome_oligomap:
         reads=INTERMEDIATES_DIR / "{sample}" / "reads_filtered_for_oligomap.fasta",
         target=INTERMEDIATES_DIR / "transcriptome_trimmed_id.fa",
     output:
-        tmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_mappings.fasta",
+        tmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_mappings.oligomap",
         report=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_report.txt",
     params:
         cluster_log=CLUSTER_LOG / "map_transcriptome_oligomap_{sample}.log",
@@ -465,10 +465,10 @@ rule map_transcriptome_oligomap:
 
 rule sort_transcriptome_oligomap:
     input:
-        tmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_mappings.fasta",
+        tmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_mappings.oligomap",
         script=SCRIPTS_DIR / "blocksort.sh",
     output:
-        sort=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_sorted.fasta",
+        sort=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_sorted.oligomap",
     params:
         cluster_log=CLUSTER_LOG / "sort_transcriptome_oligomap_{sample}.log",
     log:
@@ -492,7 +492,7 @@ rule sort_transcriptome_oligomap:
 
 rule convert_transcriptome_to_sam_oligomap:
     input:
-        sort=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_sorted.fasta",
+        sort=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_sorted.oligomap",
         script=SCRIPTS_DIR / "oligomap_output_to_sam_nh_filtered.py",
     output:
         tmap=INTERMEDIATES_DIR / "{sample}" / "oligomap_transcriptome_mappings.sam",