Fix bcftools stub to behave like program

nf-core · Sep 19, 2024 · fb8e74d · fb8e74d
1 parent cc9eb89
commit fb8e74d
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Showing 16 changed files with 332 additions and 196 deletions.
diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf
@@ -25,11 +25,7 @@ process BCFTOOLS_ANNOTATE {
     def prefix  = task.ext.prefix ?: "${meta.id}"
     def header_file = header_lines ? "--header-lines ${header_lines}" : ''
     def annotations_file = annotations ? "--annotations ${annotations}" : ''
-    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
-                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
-                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
-                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
-                    "vcf"
+    def extension = getVcfExtension(args);
     def index_command = !index ? "bcftools index $input" : ''
 
     if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
@@ -54,18 +50,12 @@ process BCFTOOLS_ANNOTATE {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
-                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
-                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
-                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
-                    "vcf"
-    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
-                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
-                args.contains("--write-index") || args.contains("-W") ? "csi" :
-                ""
+    def extension = getVcfExtension(args);
+    def index = getVcfIndex(args, extension);
     def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
-    def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
+    def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""
 
+    if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
     ${create_cmd} ${prefix}.${extension}
     ${create_index}
@@ -76,3 +66,22 @@ process BCFTOOLS_ANNOTATE {
     END_VERSIONS
     """
 }
+// Custom Functions
+String getVcfExtension(String args) {
+    return args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+        args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+        args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+        args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+        "vcf";
+}
+String getVcfIndex(String args, String extension) {
+    index = ''
+    if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
+        if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) }  && extension == 'vcf.gz') {
+            index = 'tbi'
+        } else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
+            index = 'csi'
+        }
+    }
+    return index
+}
diff --git a/modules/nf-core/bcftools/call/main.nf b/modules/nf-core/bcftools/call/main.nf
@@ -47,12 +47,9 @@ process BCFTOOLS_CALL {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
-                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
-                args.contains("--write-index") || args.contains("-W") ? "csi" :
-                ""
-
-    def create_index = index.matches("csi|tbi") ? "touch ${prefix}.vcf.gz.${index}" : ""
+    def extension = "vcf.gz"
+    def index = getVcfIndex(args, extension);
+    def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""
 
     """
     echo "" | gzip > ${prefix}.vcf.gz
@@ -64,3 +61,15 @@ process BCFTOOLS_CALL {
     END_VERSIONS
     """
 }
+// Custom Functions
+String getVcfIndex(String args, String extension) {
+    index = ''
+    if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
+        if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) }  && extension == 'vcf.gz') {
+            index = 'tbi'
+        } else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
+            index = 'csi'
+        }
+    }
+    return index
+}
diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf
@@ -38,11 +38,9 @@ process BCFTOOLS_CONCAT {
     stub:
     def args = task.ext.args   ?: ''
     def prefix   = task.ext.prefix ?: "${meta.id}"
-    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
-                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
-                args.contains("--write-index") || args.contains("-W") ? "csi" :
-                ""
-    def create_index = index.matches("csi|tbi") ? "touch ${prefix}.vcf.gz.${index}" : ""
+    def extension = "vcf.gz"
+    def index = getVcfIndex(args, extension);
+    def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""
     """
     echo "" | gzip > ${prefix}.vcf.gz
     ${create_index}
@@ -53,3 +51,14 @@ process BCFTOOLS_CONCAT {
     END_VERSIONS
     """
 }
+String getVcfIndex(String args, String extension) {
+    index = ''
+    if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
+        if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) }  && extension == 'vcf.gz') {
+            index = 'tbi'
+        } else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
+            index = 'csi'
+        }
+    }
+    return index
+}
diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf
@@ -31,18 +31,13 @@ process BCFTOOLS_CONVERT {
 
     def regions = bed ? "--regions-file $bed" : ""
     def reference = fasta ?  "--fasta-ref $fasta" : ""
-    def extension = args.contains("--output-type b")    || args.contains("-Ob")    ? "--output ${prefix}.bcf.gz" :
-                    args.contains("--output-type u")    || args.contains("-Ou")    ? "--output ${prefix}.bcf" :
-                    args.contains("--output-type z")    || args.contains("-Oz")    ? "--output ${prefix}.vcf.gz" :
-                    args.contains("--output-type v")    || args.contains("-Ov")    ? "--output ${prefix}.vcf" :
-                    args.contains("--haplegendsample")  || args.contains("-h")     ? "" :
-                    "--output ${prefix}.vcf.gz"
+    def extension = getVcfExtension(args);
 
     """
     bcftools convert \\
         $args \\
         $regions \\
-        $extension \\
+        --output ${prefix}.${extension} \\
         --threads $task.cpus \\
         $reference \\
         $input
@@ -56,18 +51,37 @@ process BCFTOOLS_CONVERT {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = getVcfExtension(args);
+    def index = getVcfIndex(args, extension);
+    def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
+    def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""
 
-    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
-                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
-                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
-                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
-                    "vcf.gz"
     """
-    touch ${prefix}.${extension}
+    ${create_cmd} ${prefix}.${extension}
+    ${create_index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
 }
+// Custom Functions
+String getVcfExtension(String args) {
+    return args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+        args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+        args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+        args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+        "vcf.gz";
+}
+String getVcfIndex(String args, String extension) {
+    index = ''
+    if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
+        if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) }  && extension == 'vcf.gz') {
+            index = 'tbi'
+        } else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
+            index = 'csi'
+        }
+    }
+    return index
+}
diff --git a/modules/nf-core/bcftools/csq/main.nf b/modules/nf-core/bcftools/csq/main.nf
@@ -51,20 +51,18 @@ process BCFTOOLS_CSQ {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     extension = getVcfExtension(args);
+    index = getVcfIndex(args, extension);
 
-    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
-                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
-                args.contains("--write-index") || args.contains("-W") ? "csi" :
-                ""
     def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
-    def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
+    def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""
 
     if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
 
     """
     ${create_cmd} ${prefix}.${extension}
     ${create_index}
 
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
@@ -79,3 +77,14 @@ String getVcfExtension(String args) {
         args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
         "vcf";
 }
+String getVcfIndex(String args, String extension) {
+    index = ''
+    if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
+        if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) }  && extension == 'vcf.gz') {
+            index = 'tbi'
+        } else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
+            index = 'csi'
+        }
+    }
+    return index
+}
diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf
@@ -23,11 +23,7 @@ process BCFTOOLS_FILTER {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
-                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
-                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
-                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
-                    "vcf"
+    extension = getVcfExtension(args);
 
     if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
 
@@ -47,17 +43,10 @@ process BCFTOOLS_FILTER {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
-                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
-                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
-                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
-                    "vcf"
-    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
-                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
-                args.contains("--write-index") || args.contains("-W") ? "csi" :
-                ""
+    extension = getVcfExtension(args);
+    def index = getVcfIndex(args, extension);
     def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
-    def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
+    def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""
 
     if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
 
@@ -71,3 +60,22 @@ process BCFTOOLS_FILTER {
     END_VERSIONS
     """
 }
+// Custom Functions
+String getVcfExtension(String args) {
+    return args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+        args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+        args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+        args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+        "vcf";
+}
+String getVcfIndex(String args, String extension) {
+    index = ''
+    if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
+        if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) }  && extension == 'vcf.gz') {
+            index = 'tbi'
+        } else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
+            index = 'csi'
+        }
+    }
+    return index
+}
diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf
@@ -38,10 +38,12 @@ process BCFTOOLS_INDEX {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def extension = args.contains("--tbi") || args.contains("-t") ? "tbi" :
-                    "csi"
+    def index = (args.contains("--tbi") || args.contains("-t")) && vcf.endsWith("vcf.gz") ? "tbi" :
+                (args.contains("--csi") || args.contains("-c")) && !vcf.endsWith("vcf") ? "csi" :
+                ""
+    def create_index = index ? "touch ${vcf}.${index}" : ""
     """
-    touch ${vcf}.${extension}
+    ${create_index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf
@@ -27,11 +27,7 @@ process BCFTOOLS_MERGE {
 
     def input = (vcfs.collect().size() > 1) ? vcfs.sort{ it.name } : vcfs
     def regions = bed ? "--regions-file $bed" : ""
-    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
-                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
-                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
-                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
-                    "vcf"
+    def extension = getVcfExtension(args);
 
     """
     bcftools merge \\
@@ -50,18 +46,10 @@ process BCFTOOLS_MERGE {
     stub:
     def args = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
-                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
-                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
-                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
-                    "vcf"
-    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
-                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
-                args.contains("--write-index") || args.contains("-W") ? "csi" :
-                ""
+    def extension = getVcfExtension(args);
+    def index = getVcfIndex(args, extension);
     def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
-    def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
-
+    def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""
     """
     ${create_cmd} ${prefix}.${extension}
     ${create_index}
@@ -72,3 +60,22 @@ process BCFTOOLS_MERGE {
     END_VERSIONS
     """
 }
+// Custom Functions
+String getVcfExtension(String args) {
+    return args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+        args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+        args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+        args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+        "vcf";
+}
+String getVcfIndex(String args, String extension) {
+    index = ''
+    if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
+        if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) }  && extension == 'vcf.gz') {
+            index = 'tbi'
+        } else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
+            index = 'csi'
+        }
+    }
+    return index
+}