From f84c36a068ed52110cf5ca08408248e3791acdf7 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Thu, 21 Nov 2024 12:20:40 -0800 Subject: [PATCH 01/11] feat: add conda pipeline env --- environment-dev.yml | 1 - environment-pipeline.yml | 16 ++++++++++++++++ 2 files changed, 16 insertions(+), 1 deletion(-) create mode 100644 environment-pipeline.yml diff --git a/environment-dev.yml b/environment-dev.yml index 1b0d9a9..0272c1a 100644 --- a/environment-dev.yml +++ b/environment-dev.yml @@ -2,7 +2,6 @@ name: longplex-nf-dev channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::nextflow=23.10.1 - conda-forge::python=3.11.0 diff --git a/environment-pipeline.yml b/environment-pipeline.yml new file mode 100644 index 0000000..521b642 --- /dev/null +++ b/environment-pipeline.yml @@ -0,0 +1,16 @@ +name: longplex-nf +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::fastqc=0.12.1 + #- bioconda::lima=2.7.1 + - bioconda::multiqc=1.21 + - bioconda::nextflow=23.10.1 + - bioconda::picard=3.2.0 + - bioconda::samtools=1.19.2 + - conda-forge::python=3.11.0 + - conda-forge::pip=22.3.1 + - conda-forge::r-base=4.3.1 + - pip: + - git+https://github.com/seqwell/longplexpy@0.1.0 From 8861e73b7f9c27df59cbe4947a7a7e8f437a6419 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Thu, 21 Nov 2024 12:25:17 -0800 Subject: [PATCH 02/11] feat: add conda profile --- nextflow.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/nextflow.config b/nextflow.config index ce4af8e..911ddce 100644 --- a/nextflow.config +++ b/nextflow.config @@ -130,6 +130,11 @@ profiles { docker.enabled = true } + conda { + conda.enabled = true + process.conda = 'environment-pipeline.yml' + } + singularity { singularity.enabled = true } From bb0214cad8278a622537b7cb2b1064da1fe04f48 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Thu, 21 Nov 2024 14:06:40 -0800 Subject: [PATCH 03/11] fix: add r-dependencies --- environment-pipeline.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/environment-pipeline.yml b/environment-pipeline.yml index 521b642..bd7ee7e 100644 --- a/environment-pipeline.yml +++ b/environment-pipeline.yml @@ -12,5 +12,8 @@ dependencies: - conda-forge::python=3.11.0 - conda-forge::pip=22.3.1 - conda-forge::r-base=4.3.1 + - conda-forge::r-dplyr=1.1.4 + - conda-forge::r-purrr=1.0.2 + - pip: - git+https://github.com/seqwell/longplexpy@0.1.0 From 071c8735e72e58c6e919503680f005b0dcaf0ec9 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Thu, 21 Nov 2024 14:07:55 -0800 Subject: [PATCH 04/11] fix: enable lima --- environment-pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment-pipeline.yml b/environment-pipeline.yml index bd7ee7e..9d58f47 100644 --- a/environment-pipeline.yml +++ b/environment-pipeline.yml @@ -4,7 +4,7 @@ channels: - bioconda dependencies: - bioconda::fastqc=0.12.1 - #- bioconda::lima=2.7.1 + - bioconda::lima=2.7.1 - bioconda::multiqc=1.21 - bioconda::nextflow=23.10.1 - bioconda::picard=3.2.0 From cb83b716263763de3d704cb7aded4357045dc9e3 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Thu, 21 Nov 2024 14:14:34 -0800 Subject: [PATCH 05/11] fix: add r packages --- environment-pipeline.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/environment-pipeline.yml b/environment-pipeline.yml index 9d58f47..9f68e1b 100644 --- a/environment-pipeline.yml +++ b/environment-pipeline.yml @@ -11,9 +11,10 @@ dependencies: - bioconda::samtools=1.19.2 - conda-forge::python=3.11.0 - conda-forge::pip=22.3.1 - - conda-forge::r-base=4.3.1 + - conda-forge::r-base=4.3.3 - conda-forge::r-dplyr=1.1.4 - conda-forge::r-purrr=1.0.2 + - conda-forge::readr=2.1.5 - pip: - git+https://github.com/seqwell/longplexpy@0.1.0 From 78484904a916343ed360791e6fa12dd7097e04f5 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Thu, 21 Nov 2024 14:15:56 -0800 Subject: [PATCH 06/11] fix: typo --- environment-pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment-pipeline.yml b/environment-pipeline.yml index 9f68e1b..60cb001 100644 --- a/environment-pipeline.yml +++ b/environment-pipeline.yml @@ -14,7 +14,7 @@ dependencies: - conda-forge::r-base=4.3.3 - conda-forge::r-dplyr=1.1.4 - conda-forge::r-purrr=1.0.2 - - conda-forge::readr=2.1.5 + - conda-forge::r-readr=2.1.5 - pip: - git+https://github.com/seqwell/longplexpy@0.1.0 From 4cc855d59d65a5ab5fb95631931364c1242d3023 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Thu, 21 Nov 2024 14:19:49 -0800 Subject: [PATCH 07/11] fix: add stringr --- environment-pipeline.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment-pipeline.yml b/environment-pipeline.yml index 60cb001..a89e462 100644 --- a/environment-pipeline.yml +++ b/environment-pipeline.yml @@ -15,6 +15,7 @@ dependencies: - conda-forge::r-dplyr=1.1.4 - conda-forge::r-purrr=1.0.2 - conda-forge::r-readr=2.1.5 + - conda-forge::r-stringr=1.5.1 - pip: - git+https://github.com/seqwell/longplexpy@0.1.0 From dc5c0a960ff45a0f4a9c488018efc99512049cf3 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Thu, 21 Nov 2024 14:23:15 -0800 Subject: [PATCH 08/11] fix: add tidyr --- environment-pipeline.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment-pipeline.yml b/environment-pipeline.yml index a89e462..f355bc3 100644 --- a/environment-pipeline.yml +++ b/environment-pipeline.yml @@ -16,6 +16,7 @@ dependencies: - conda-forge::r-purrr=1.0.2 - conda-forge::r-readr=2.1.5 - conda-forge::r-stringr=1.5.1 + - conda-forge::r-tidyr=1.3.1 - pip: - git+https://github.com/seqwell/longplexpy@0.1.0 From 20915de3aabce2c7b93781d54d363ff24c99b972 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Thu, 21 Nov 2024 15:05:25 -0800 Subject: [PATCH 09/11] docs: update readme --- README.md | 17 +++++++++++++++++ environment-pipeline.yml | 1 - 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index b3bbe82..c57a939 100644 --- a/README.md +++ b/README.md @@ -69,6 +69,7 @@ Several profiles are available and can be selected with the `-profile` option at - `apptainer` - `aws` +- `conda` - `docker` - `singularity` @@ -86,6 +87,8 @@ nextflow run \ # Running Test Data +## With Docker + The pipeline can be run using included test data with: ```bash @@ -100,6 +103,20 @@ nextflow run \ -resume ``` +## With Conda + +```bash +nextflow run \ + -profile conda \ + main.nf \ + -c nextflow.config \ + --pool_sheet "${PWD}/tests/pool_sheet.csv" \ + --output "${PWD}/test_output" \ + -with-report \ + -with-trace \ + -resume +``` + ## Expected Outputs ```console diff --git a/environment-pipeline.yml b/environment-pipeline.yml index f355bc3..2c55fc3 100644 --- a/environment-pipeline.yml +++ b/environment-pipeline.yml @@ -6,7 +6,6 @@ dependencies: - bioconda::fastqc=0.12.1 - bioconda::lima=2.7.1 - bioconda::multiqc=1.21 - - bioconda::nextflow=23.10.1 - bioconda::picard=3.2.0 - bioconda::samtools=1.19.2 - conda-forge::python=3.11.0 From 4febd2476b311a4d14192a13d618b1139fe3164d Mon Sep 17 00:00:00 2001 From: znorgaard Date: Thu, 21 Nov 2024 15:08:49 -0800 Subject: [PATCH 10/11] docs: update readme --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index c57a939..0483a81 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,8 @@ The final output from this pipeline includes Lima output files, demultiplexed BA ## Dependencies -This pipeline requires installation of [Nextflow](https://www.nextflow.io/docs/latest/install.html) and a containerization platform such as [Docker](https://docs.docker.com/engine/install/). +This pipeline requires installation of [Nextflow](https://www.nextflow.io/docs/latest/install.html). +It also requires installation of either a containerization platform such as [Docker](https://docs.docker.com/engine/install/) or a package manager such as [conda/mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html). ## Docker Containers From 7260f2756d9e859aca33c04a32204e035109b859 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Thu, 21 Nov 2024 15:10:17 -0800 Subject: [PATCH 11/11] docs: update readme --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 0483a81..d7036b7 100644 --- a/README.md +++ b/README.md @@ -36,6 +36,10 @@ All docker containers used in this pipeline are publicly available. - *fastqc*: quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0 - *multiqc*: quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0 +## Conda Environment + +The conda environment is defined in `environment-pipeline.yml` and will be built automatically if the pipeline is run with `-profile conda`. + # How to run the pipeline: ## Required Parameters