From 7fbfd2d6cb92907e9c981d04f7bf5a408a3f8e7d Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 23 Jan 2020 11:36:21 +0100
Subject: [PATCH] add samtools faidx to index fasta file

---
 tools/samtools/faidx/main.nf              | 16 ++++++++++++++
 tools/samtools/faidx/meta.yml             | 27 +++++++++++++++++++++++
 tools/samtools/faidx/test/main.nf         | 13 +++++++++++
 tools/samtools/faidx/test/nextflow.config |  2 ++
 4 files changed, 58 insertions(+)
 create mode 100644 tools/samtools/faidx/main.nf
 create mode 100644 tools/samtools/faidx/meta.yml
 create mode 100644 tools/samtools/faidx/test/main.nf
 create mode 100644 tools/samtools/faidx/test/nextflow.config

diff --git a/tools/samtools/faidx/main.nf b/tools/samtools/faidx/main.nf
new file mode 100644
index 00000000..458a5ab8
--- /dev/null
+++ b/tools/samtools/faidx/main.nf
@@ -0,0 +1,16 @@
+process samtools_faidx {
+    tag {fasta}
+
+    container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
+
+    input:
+        path(fasta)
+
+    output:
+        path("${fasta}.fai")
+
+    script:
+    """
+    samtools faidx ${fasta}
+    """
+}
diff --git a/tools/samtools/faidx/meta.yml b/tools/samtools/faidx/meta.yml
new file mode 100644
index 00000000..1e402057
--- /dev/null
+++ b/tools/samtools/faidx/meta.yml
@@ -0,0 +1,27 @@
+name: samtools faidx
+description: index a fasta file
+keywords:
+    - faidx
+tools:
+    - samtools:
+        description: |
+            SAMtools is a set of utilities for interacting with and post-processing
+            short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+            These files are generated as output by short read aligners like BWA.
+        homepage: http://www.htslib.org/
+        documentation: hhttp://www.htslib.org/doc/samtools.html
+        doi: 10.1093/bioinformatics/btp352
+input:
+    -
+        - input:
+            type: file
+            description: Input fasta file
+            pattern: *.{fasta,fa}
+output:
+    -
+        - faidx:
+            type: file
+            description: samtools index fasta file
+            pattern: *.fasta.fai
+authors:
+    - @maxulysse
\ No newline at end of file
diff --git a/tools/samtools/faidx/test/main.nf b/tools/samtools/faidx/test/main.nf
new file mode 100644
index 00000000..f01ab6c9
--- /dev/null
+++ b/tools/samtools/faidx/test/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+nextflow.preview.dsl = 2
+include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
+include '../main.nf' params(params)
+
+// Define input channels
+input = '../../../test-datasets/tools/bwa/index/input/reference.fasta'
+
+// Run the workflow
+workflow {
+    samtools_faidx(input)
+    // .check_output()
+}
diff --git a/tools/samtools/faidx/test/nextflow.config b/tools/samtools/faidx/test/nextflow.config
new file mode 100644
index 00000000..c137a138
--- /dev/null
+++ b/tools/samtools/faidx/test/nextflow.config
@@ -0,0 +1,2 @@
+docker.enabled = true
+params.outdir = './results'