From 81ed0e0ff2a138cd65146d167f614fa4f5871c8b Mon Sep 17 00:00:00 2001
From: Kevin <klkeys@users.noreply.github.com>
Date: Sat, 23 Oct 2021 09:30:10 -0700
Subject: [PATCH] added meta.yml for umitools (#860)

* added meta.yml for umitools

* Update modules/umitools/dedup/meta.yml

type: list --> type: file

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/umitools/dedup/meta.yml

aww thanks @drpateh :D

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/umitools/dedup/meta.yml

module can only handle one BAM at a time, ergo

BAM files --> BAM file

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update meta.yml

added `pattern` for input `bam` and `bai`

* removed trailing whitespace to appease linter

* added license to new meta.yml files

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/umitools/dedup/meta.yml   | 47 +++++++++++++++++++++++++++++++
 modules/umitools/extract/meta.yml | 46 ++++++++++++++++++++++++++++++
 2 files changed, 93 insertions(+)
 create mode 100644 modules/umitools/dedup/meta.yml
 create mode 100644 modules/umitools/extract/meta.yml

diff --git a/modules/umitools/dedup/meta.yml b/modules/umitools/dedup/meta.yml
new file mode 100644
index 00000000..f89cc1ea
--- /dev/null
+++ b/modules/umitools/dedup/meta.yml
@@ -0,0 +1,47 @@
+name: umitools_dedup
+description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
+keywords:
+    - umitools
+    - deduplication
+tools:
+    - umi_tools:
+        description: >
+            UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)
+            and single cell RNA-Seq cell barcodes
+        documentation: https://umi-tools.readthedocs.io/en/latest/
+        license: ['MIT']
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: |
+            BAM file containing reads to be deduplicated via UMIs.
+        pattern: "*.{bam}"
+    - bai:
+        type: file
+        description: |
+            BAM index files corresponding to the input BAM file.
+        pattern: "*.{bai}"
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM file with deduplicated UMIs.
+        pattern: "*.{bam}"
+    - versions:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+    - "@drpatelh"
+    - "@grst"
+    - "@klkeys"
diff --git a/modules/umitools/extract/meta.yml b/modules/umitools/extract/meta.yml
new file mode 100644
index 00000000..ae6f9fee
--- /dev/null
+++ b/modules/umitools/extract/meta.yml
@@ -0,0 +1,46 @@
+name: umitools_extract
+description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place
+keywords:
+    - umitools
+    - extract
+tools:
+    - umi_tools:
+        description: >
+            UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)
+            and single cell RNA-Seq cell barcodes
+        documentation: https://umi-tools.readthedocs.io/en/latest/
+        license: ['MIT']
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: list
+        description: |
+            List of input FASTQ files whose UMIs will be extracted.
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: Extracted FASTQ files. |
+            For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. |
+            For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz.
+        pattern: "*.{fastq.gz}"
+    - log:
+        type: file
+        description: Logfile for umi_tools
+        pattern: "*.{log}"
+    - versions:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+    - "@drpatelh"
+    - "@grst"