From 20ebb89ff97a2665106be9cace5ccb9aa4eed1be Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 10:52:40 +0200
Subject: [PATCH] update to long args

---
 modules/picard/addorreplacereadgroups/main.nf   | 10 +++++-----
 modules/picard/cleansam/main.nf                 |  4 ++--
 modules/picard/createsequencedictionary/main.nf |  4 ++--
 modules/picard/fixmateinformation/main.nf       |  4 ++--
 modules/picard/liftovervcf/main.nf              |  6 +++---
 modules/picard/markduplicates/main.nf           |  6 +++---
 modules/picard/mergesamfiles/main.nf            |  4 ++--
 modules/picard/sortvcf/main.nf                  |  4 ++--
 8 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/modules/picard/addorreplacereadgroups/main.nf b/modules/picard/addorreplacereadgroups/main.nf
index 55200d2e..fd102f67 100644
--- a/modules/picard/addorreplacereadgroups/main.nf
+++ b/modules/picard/addorreplacereadgroups/main.nf
@@ -38,11 +38,11 @@ process PICARD_ADDORREPLACEREADGROUPS {
         -Xmx${avail_mem}g \\
         --INPUT ${bam} \\
         --OUTPUT ${prefix}.bam \\
-        -ID ${ID} \\
-        -LB ${LIBRARY} \\
-        -PL ${PLATFORM} \\
-        -PU ${BARCODE} \\
-        -SM ${SAMPLE} \\
+        --RGID ${ID} \\
+        --RGLB ${LIBRARY} \\
+        --RGPL ${PLATFORM} \\
+        --RGPU ${BARCODE} \\
+        --RGSM ${SAMPLE} \\
         --CREATE_INDEX true
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/picard/cleansam/main.nf b/modules/picard/cleansam/main.nf
index 4cd4db58..62989565 100644
--- a/modules/picard/cleansam/main.nf
+++ b/modules/picard/cleansam/main.nf
@@ -31,8 +31,8 @@ process PICARD_CLEANSAM {
         -Xmx${avail_mem}g \\
         CleanSam  \\
         ${args} \\
-        -I ${bam} \\
-        -O ${prefix}.bam
+        --INPUT ${bam} \\
+        --OUTPUT ${prefix}.bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/createsequencedictionary/main.nf b/modules/picard/createsequencedictionary/main.nf
index 3a8bb62a..735cc97b 100644
--- a/modules/picard/createsequencedictionary/main.nf
+++ b/modules/picard/createsequencedictionary/main.nf
@@ -31,8 +31,8 @@ process PICARD_CREATESEQUENCEDICTIONARY {
         -Xmx${avail_mem}g \\
         CreateSequenceDictionary  \\
         $args \\
-        -R $fasta \\
-        -O ${prefix}.dict
+        --REFERENCE_SEQUENCE $fasta \\
+        --OUTPUT ${prefix}.dict
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/fixmateinformation/main.nf b/modules/picard/fixmateinformation/main.nf
index 1993e4fd..539b1082 100644
--- a/modules/picard/fixmateinformation/main.nf
+++ b/modules/picard/fixmateinformation/main.nf
@@ -31,8 +31,8 @@ process PICARD_FIXMATEINFORMATION {
     picard \\
         FixMateInformation \\
         -Xmx${avail_mem}g \\
-        -I ${bam} \\
-        -O ${prefix}.bam \\
+        --INPUT ${bam} \\
+        --OUTPUT ${prefix}.bam \\
         --VALIDATION_STRINGENCY ${STRINGENCY}
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/picard/liftovervcf/main.nf b/modules/picard/liftovervcf/main.nf
index ea3f4cb7..c92abfeb 100644
--- a/modules/picard/liftovervcf/main.nf
+++ b/modules/picard/liftovervcf/main.nf
@@ -35,11 +35,11 @@ process PICARD_LIFTOVERVCF {
         -Xmx${avail_mem}g \\
         LiftoverVcf \\
         $args \\
-        -I $input_vcf \\
-        -O ${prefix}.lifted.vcf.gz \\
+        --INPUT $input_vcf \\
+        --OUTPUT ${prefix}.lifted.vcf.gz \\
         --CHAIN $chain \\
         --REJECT ${prefix}.unlifted.vcf.gz \\
-        -R $fasta
+        --REFERENCE_SEQUENCE $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf
index 58b6b88a..1565c647 100644
--- a/modules/picard/markduplicates/main.nf
+++ b/modules/picard/markduplicates/main.nf
@@ -33,9 +33,9 @@ process PICARD_MARKDUPLICATES {
         -Xmx${avail_mem}g \\
         MarkDuplicates \\
         $args \\
-        -I $bam \\
-        -O ${prefix}.bam \\
-        -M ${prefix}.MarkDuplicates.metrics.txt
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.bam \\
+        --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf
index 7b0185cd..1e32c63a 100644
--- a/modules/picard/mergesamfiles/main.nf
+++ b/modules/picard/mergesamfiles/main.nf
@@ -33,8 +33,8 @@ process PICARD_MERGESAMFILES {
             -Xmx${avail_mem}g \\
             MergeSamFiles \\
             $args \\
-            ${'INPUT='+bam_files.join(' INPUT=')} \\
-            OUTPUT=${prefix}.bam
+            ${'--INPUT '+bam_files.join(' --INPUT ')} \\
+            --OUTPUT ${prefix}.bam
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             picard: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
diff --git a/modules/picard/sortvcf/main.nf b/modules/picard/sortvcf/main.nf
index 5fe0ecfd..fb8dbb79 100644
--- a/modules/picard/sortvcf/main.nf
+++ b/modules/picard/sortvcf/main.nf
@@ -22,8 +22,8 @@ process PICARD_SORTVCF {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def seq_dict = sequence_dict ? "-SEQUENCE_DICTIONARY $sequence_dict" : ""
-    def reference = reference ? "-REFERENCE_SEQUENCE $reference" : ""
+    def seq_dict = sequence_dict ? "--SEQUENCE_DICTIONARY $sequence_dict" : ""
+    def reference = reference ? "--REFERENCE_SEQUENCE $reference" : ""
     def avail_mem = 3
     if (!task.memory) {
         log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'