From bfd426e764c22d68d22c7440d603cbcf72973326 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 5 Jan 2023 16:23:05 +0100
Subject: [PATCH] Remove usages of deprecated Channel.from method and prepare
 release

---
 CHANGELOG.md       | 18 ++++++++++++++++++
 nextflow.config    |  2 +-
 workflows/sarek.nf |  6 +++---
 3 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 54bdb8c847..04d33c3976 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,24 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.1.2](https://github.com/nf-core/sarek/releases/tag/3.1.2) - Lesser Lule River
+
+Lesser Lule River is English for Lilla Luleälven
+
+### Added
+
+### Changed
+
+### Fixed
+
+- [#905](https://github.com/nf-core/sarek/pull/905) - Remove usages of deprecated `Channel.from` method
+
+### Deprecated
+
+### Removed
+
+### Dependencies
+
 ## [3.1.1](https://github.com/nf-core/sarek/releases/tag/3.1.1) - Lilla Luleälven
 
 Lilla Luleälven river's main affluent is Rapaätno.
diff --git a/nextflow.config b/nextflow.config
index a11a1a4dcd..1631195706 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -280,7 +280,7 @@ manifest {
     description     = 'An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version = '3.1.1'
+    version = '3.1.2'
     doi             = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683'
 }
 
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index c67c5789c1..1313be9c08 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -1081,7 +1081,7 @@ workflow SAREK {
         ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
         ch_multiqc_files = ch_multiqc_files.mix(ch_reports.collect().ifEmpty([]))
 
-        ch_multiqc_configs = Channel.from(ch_multiqc_config).mix(ch_multiqc_custom_config).ifEmpty([])
+        ch_multiqc_configs = ch_multiqc_config.mix(ch_multiqc_custom_config).ifEmpty([])
 
         MULTIQC (
             ch_multiqc_files.collect(),
@@ -1134,7 +1134,7 @@ def extract_csv(csv_file) {
     def patient_sample_lane_combinations_in_samplesheet = []
     def sample2patient = [:]
 
-    Channel.from(csv_file).splitCsv(header: true)
+    Channel.of(csv_file).splitCsv(header: true)
         .map{ row ->
             if (params.step == "mapping") {
                 if ( !row.lane ) {  // This also handles the case where the lane is left as an empty string
@@ -1161,7 +1161,7 @@ def extract_csv(csv_file) {
     sample_count_normal = 0
     sample_count_tumor = 0
 
-    Channel.from(csv_file).splitCsv(header: true)
+    Channel.of(csv_file).splitCsv(header: true)
         //Retrieves number of lanes by grouping together by patient and sample and counting how many entries there are for this combination
         .map{ row ->
             sample_count_all++