--- a/macros.xml	Sat Sep 28 16:40:30 2024 +0000
+++ b/macros.xml	Sat Oct 05 13:08:04 2024 +0000
@@ -4,8 +4,8 @@
     <!-- macros applying to all umi_tools -->
 
     <token name="@TOOL_VERSION@">1.1.5</token>
-    <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">21.01</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">23.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">umi_tools</requirement>
@@ -104,8 +104,8 @@
                 <expand macro="barcode1_macro"/>
             </when>
             <when value="paired">
-                <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
-                <param name="input_read2" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
+                <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Forward reads in FASTQ format" />
+                <param name="input_read2" type="data" format="@FASTQ_FORMATS@" label="Reverse reads in FASTQ format" />
                 <expand macro="barcode1_macro"/>
                 <expand macro="barcode2_macro"/>
                 <yield/>
@@ -152,11 +152,11 @@
 
     <token name="@LINK_SAM_BAM_INPUT@"><![CDATA[
         #if $input.is_of_type("sam"):
-            ## TODO dedup has problems with SAM input in some cases
+            ## sam input is not supported for paired data
             ## https://github.com/CGATOxford/UMI-tools/issues/483
-            ## so convert it to sorted BAM for now
+            ## so convert it to sorted BAM
             ## #set $input_file = $input
-            samtools sort --no-PG '$input' > 'input.bam' &&
+            samtools sort --no-PG '$input' -O BAM > 'input.bam' &&
             samtools index -b 'input.bam' &&
             #set $input_file = 'input.bam'
         #else:
@@ -166,7 +166,7 @@
         #end if
     ]]></token>
     <token name="@SET_INPUT_TYPE@"><![CDATA[
-        ## TODO see comment in LINK_SAM_BAM_INPUT
+        ## see comment in LINK_SAM_BAM_INPUT
         ## #if $input.is_of_type("sam"):
         ##     --in-sam
         ## #end if
@@ -511,12 +511,12 @@
             <param argument="--assigned-status-tag" type="text" optional="true" label="Bam tag describing whether read is assigned to a gene" help="By default, this is set as the same tag as --gene-tag">
                 <expand macro="sanitize_tag" />
             </param>
-            <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
+            <param argument="--skip-tags-regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
                 <expand macro="barcode_sanitizer" />
             </param>
             <param argument="--per-contig" type="boolean" truevalue="--per-contig" falsevalue="" label="Deduplicate per contig" help="Field 3 in BAM; RNAME. All reads with the same contig will be considered to have the same alignment position. This is useful if your library prep generates PCR duplicates with non identical alignment positions such as CEL-Seq. In this case, you would align to a reference transcriptome with one transcript per gene" />
             <param argument="--gene-transcript-map" type="data" format="tabular" optional="true" label="Tabular file mapping genes to transripts" />
-            <param argument="--per-cell" name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" label="Group reads only if they have the same cell barcode" />
+            <param argument="--per-cell" type="boolean" truevalue="--per-cell" falsevalue="" label="Group reads only if they have the same cell barcode" />
         </section>
     </xml>
     <token name="@SC_OPTIONS@"><![CDATA[