update hifiasm module to support --ul with ONT reads (#7336)

* update hifiasm module to support --ul with ONT reads * update meta.yml with new inputs * update test * renamed reads to reads_hifi * use correct variable * long_reads and ul_reads as inputs * long_reads and ul_reads as inputs --------- Co-authored-by: Matthias Hörtenhuber <[email protected]>
nf-core · Jan 20, 2025 · ea86101 · ea86101
1 parent 25ddc0b
commit ea86101
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Showing 3 changed files with 28 additions and 14 deletions.
diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf
@@ -8,7 +8,7 @@ process HIFIASM {
         'biocontainers/hifiasm:0.24.0--h5ca1c30_0' }"
 
     input:
-    tuple val(meta) , path(reads)
+    tuple val(meta) , path(long_reads)        , path(ul_reads)
     tuple val(meta1), path(paternal_kmer_dump), path(maternal_kmer_dump)
     tuple val(meta2), path(hic_read1)         , path(hic_read2)
 
@@ -32,6 +32,8 @@ process HIFIASM {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def ultralong = ul_reads ? "--ul ${ul_reads}" : ""
+
     if ((paternal_kmer_dump) && (maternal_kmer_dump) && (hic_read1) && (hic_read2)) {
         error "Hifiasm Trio-binning and Hi-C integrated should not be used at the same time"
     } else if ((paternal_kmer_dump) && !(maternal_kmer_dump)) {
@@ -46,7 +48,8 @@ process HIFIASM {
             -t $task.cpus \\
             -1 $paternal_kmer_dump \\
             -2 $maternal_kmer_dump \\
-            $reads \\
+            $ultralong \\
+            $long_reads \\
             2> >( tee ${prefix}.stderr.log >&2 )
 
 
@@ -67,7 +70,8 @@ process HIFIASM {
             -t $task.cpus \\
             --h1 $hic_read1 \\
             --h2 $hic_read2 \\
-            $reads \\
+            $ultralong \\
+            $long_reads \\
             2> >( tee ${prefix}.stderr.log >&2 )
 
 
@@ -82,7 +86,8 @@ process HIFIASM {
             $args \\
             -o ${prefix}.asm \\
             -t $task.cpus \\
-            $reads \\
+            $ultralong \\
+            $long_reads \\
             2> >( tee ${prefix}.stderr.log >&2 )
 
         cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/hifiasm/meta.yml b/modules/nf-core/hifiasm/meta.yml
@@ -22,10 +22,12 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - reads:
+    - long_reads:
         type: file
-        description: FASTQ file with PacBio HiFi reads
-        pattern: "*.{fastq}"
+        description: Long reads PacBio HiFi reads or ONT reads (requires ext.arg '--ont').
+    - ul_reads:
+        type: file
+        description: ONT long reads to use with --ul.
   - - meta1:
         type: map
         description: |

diff --git a/modules/nf-core/hifiasm/tests/main.nf.test b/modules/nf-core/hifiasm/tests/main.nf.test
@@ -15,7 +15,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id : 'test'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [],
@@ -55,7 +56,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id : 'test'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [ id : 'test' ],
@@ -94,7 +96,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id : 'test'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [ id : 'test' ],
@@ -132,7 +135,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id : 'test'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [ id : 'test' ],
@@ -158,7 +162,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id : 'test'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [ id : 'test'],
@@ -180,7 +185,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id : 'test'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true),
+                    []
                 ]
                 input[1] = []
                 input[2] = [
@@ -204,7 +210,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id : 'test'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [],