From c3f5308254ac0777acfd7d081ef04fae92f53ebf Mon Sep 17 00:00:00 2001
From: Pablo Riesgo Ferreiro <priesgoferreiro@gmail.com>
Date: Mon, 8 Nov 2021 21:40:52 +0100
Subject: [PATCH] define conda dependencies at process level

---
 Dockerfile         | 13 -------------
 environment.yml    | 11 -----------
 modules/bwa_aln.nf |  9 +++++++++
 modules/bwa_mem.nf |  5 +++++
 modules/fastp.nf   |  6 ++++++
 nextflow.config    |  5 +++--
 6 files changed, 23 insertions(+), 26 deletions(-)
 delete mode 100644 Dockerfile
 delete mode 100644 environment.yml

diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index e14b36c..0000000
--- a/Dockerfile
+++ /dev/null
@@ -1,13 +0,0 @@
-FROM nfcore/base:1.9
-LABEL authors="Pablo Riesgo Ferreiro" \
-      description="Docker image containing all software requirements for the TRON-bioinformatics/tron-bwa pipeline"
-
-# Install the conda environment
-COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
-
-# Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/tronflow-bwa-1.1.0/bin:$PATH
-
-# Dump the details of the installed packages to a file for posterity
-RUN conda env export --name tronflow-bwa-1.1.0 > tronflow-bwa-1.1.0.yml
\ No newline at end of file
diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index ef625c8..0000000
--- a/environment.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-# You can use this file to create a conda environment for this pipeline:
-#   conda env create -f environment.yml
-name: tronflow-bwa-1.5.0
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::bwa=0.7.17
-  - bioconda::samtools=1.12
-  - bioconda::fastp=0.20.1
\ No newline at end of file
diff --git a/modules/bwa_aln.nf b/modules/bwa_aln.nf
index 4779262..3ed7a27 100644
--- a/modules/bwa_aln.nf
+++ b/modules/bwa_aln.nf
@@ -1,6 +1,7 @@
 params.cpus = 8
 params.memory = "8g"
 params.reference = false
+params.enable_conda = false
 
 
 process BWA_ALN {
@@ -8,6 +9,8 @@ process BWA_ALN {
     memory "${params.memory}"
     tag "${name}"
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+
     input:
         tuple val(name), file(fastq)
 
@@ -25,6 +28,8 @@ process BWA_SAMPE {
     tag "${name}"
     publishDir params.output, mode: "move"
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq1), file(sai1), file(fastq2), file(sai2)
@@ -43,6 +48,8 @@ process BWA_SAMSE {
     tag "${name}"
     publishDir params.output, mode: "move"
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq), file(sai)
@@ -61,6 +68,8 @@ process BWA_ALN_INCEPTION {
     tag "${name}"
     publishDir params.output, mode: "move"
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq1), file(fastq2)
diff --git a/modules/bwa_mem.nf b/modules/bwa_mem.nf
index 2989410..d20c165 100644
--- a/modules/bwa_mem.nf
+++ b/modules/bwa_mem.nf
@@ -1,6 +1,7 @@
 params.cpus = 8
 params.memory = "8g"
 params.reference = false
+params.enable_conda = false
 
 
 process BWA_MEM {
@@ -9,6 +10,8 @@ process BWA_MEM {
     tag "${name}"
     publishDir params.output, mode: "move"
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq1), file(fastq2)
@@ -27,6 +30,8 @@ process BWA_MEM_SE {
     tag "${name}"
     publishDir params.output, mode: "move"
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq)
diff --git a/modules/fastp.nf b/modules/fastp.nf
index aff12e8..49e05ec 100644
--- a/modules/fastp.nf
+++ b/modules/fastp.nf
@@ -1,6 +1,8 @@
 params.memory = "3g"
 params.cpus = 1
 params.output = "."
+params.enable_conda = false
+params.enable_docker = true
 
 
 process FASTP_PAIRED {
@@ -8,6 +10,8 @@ process FASTP_PAIRED {
     memory params.memory
     publishDir "${params.output}", mode: "copy", pattern: "*fastp_stats*"
 
+    conda (params.enable_conda ? "bioconda::fastp=0.20.1" : null)
+
     input:
         tuple val(name), file(fastq1), file(fastq2)
 
@@ -34,6 +38,8 @@ process FASTP_SINGLE {
     memory params.memory
     publishDir "${params.output}", mode: "copy", pattern: "*fastp_stats*"
 
+    conda (params.enable_conda ? "bioconda::fastp=0.20.1" : null)
+
     input:
         tuple val(name), file(fastq1)
 
diff --git a/nextflow.config b/nextflow.config
index b6ac921..1fc94a7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -4,9 +4,10 @@
  * -------------------------------------------------
  */
 
-
 profiles {
-  conda { process.conda = "$baseDir/environment.yml" }
+  conda {
+    params.enable_conda = true
+  }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   test {
     params.input_files = "test_data/test_input_paired.txt"