samtools fixes (galaxyproject#4598)

* allow 4 diff for bam files an additional diff line is due to more processors used xref galaxyproject#4490 * link fasta file because a .fai is written next to it leads to a failing ci job due to galaxyproject/planemo#1199
EngyNasr · Jun 21, 2022 · 84db51c · 84db51c
1 parent e5b0861
commit 84db51c
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Showing 2 changed files with 15 additions and 9 deletions.
diff --git a/tool_collections/samtools/samtools_markdup/samtools_markdup.xml b/tool_collections/samtools/samtools_markdup/samtools_markdup.xml
@@ -1,4 +1,4 @@
-<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@" profile="@PROFILE@" >
+<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" >
     <description>marks duplicate alignments</description>
     <macros>
         <import>macros.xml</import>
@@ -19,6 +19,12 @@
     ln -s '$bamfile' coordsort.sam &&
 #end if
 
+## copy fasta reference if needed
+## because samtools will try to write a .fai file next to it
+#if $output_options.output_format.select_oformat == "CRAM"
+    ln -s '$output_options.output_format.ref_file' ref_file.fa &&
+#end if
+
 samtools markdup
 
 -@ \$addthreads
@@ -39,7 +45,7 @@ $include_fails
 #end if
 -O $output_options.output_format.select_oformat
 #if $output_options.output_format.select_oformat == "CRAM"
-    --reference '$output_options.output_format.ref_file'
+    --reference ref_file.fa
 #end if
 coordsort.sam
 '$output'

diff --git a/tool_collections/samtools/samtools_stats/samtools_stats.xml b/tool_collections/samtools/samtools_stats/samtools_stats.xml
@@ -1,4 +1,4 @@
-<tool id="samtools_stats" name="Samtools stats" version="2.0.3" profile="@PROFILE@">
+<tool id="samtools_stats" name="Samtools stats" version="2.0.4" profile="@PROFILE@">
     <description>generate statistics for BAM dataset</description>
     <macros>
         <import>macros.xml</import>
@@ -170,7 +170,7 @@
                 <param name="addref_select" value="history" />
                 <param name="ref" value="test.fa" ftype="fasta" />
             </conditional>
-            <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="2" />
+            <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/1.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);-->
         <test>
@@ -179,7 +179,7 @@
                 <param name="addref_select" value="history" />
                 <param name="ref" value="test.fa" ftype="fasta" />
             </conditional>
-            <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="2" />
+            <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
         <!-- test_cmd($opts,out=>'stat/3.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);-->
@@ -192,7 +192,7 @@
                 <param name="addref_select" value="history" />
                 <param name="ref" value="test.fa" ftype="fasta" />
             </conditional>
-            <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="2" />
+            <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
         <!-- test_cmd($opts,out=>'stat/7.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); -->
@@ -223,7 +223,7 @@
                 <param name="regions_repeat_1|region" value="ref1:30-46"/>
                 <param name="regions_repeat_2|region" value="ref1:39-56"/>
             </conditional>
-            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="2" />
+            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix);
 -->
@@ -252,7 +252,7 @@
                 <param name="regions_repeat_2|region" value="ref1:39-56"/>
             </conditional>
             <param name="cov_threshold" value="4" />
-            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="2" />
+            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); -->
         <test>
@@ -311,7 +311,7 @@
                 <param name="addref_select" value="history" />
                 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
             </conditional>
-            <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="2" />
+            <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" />
         </test>
         <test>
             <param name="input" value="samtools_stats_input.bam" ftype="bam" />