Merge pull request #3 from nf-core/dev

pull nf-core
bigbio · Apr 9, 2022 · 6da652f · 6da652f
2 parents d3b78e7 + 4d3b3e6
commit 6da652f
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# ![nf-core/quantms](docs/images/nf-core/quantms_logo_light.png#gh-light-mode-only) ![nf-core/quantms](docs/images/nf-core/quantms_logo_dark.png#gh-dark-mode-only)
+# ![nf-core/quantms](docs/images/nf-core-quantms_logo_light.png#gh-light-mode-only) ![nf-core/quantms](docs/images/nf-core-quantms_logo_dark.png#gh-dark-mode-only)
 
 [![GitHub Actions CI Status](https://github.com/nf-core/quantms/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/quantms/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/quantms/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/quantms/actions?query=workflow%3A%22nf-core+linting%22)
@@ -77,7 +77,7 @@ DIA-LFQ:
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
    ```console
-   nextflow run nf-core/quantms -profile test,YOURPROFILE --input project.sdrf.tsv --database protein.fasta
+   nextflow run nf-core/quantms -profile test,YOURPROFILE --input project.sdrf.tsv --database protein.fasta --outdir <OUTDIR>
    ```
 
    Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
@@ -97,7 +97,7 @@ DIA-LFQ:
    <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
 
    ```console
-   nextflow run nf-core/quantms -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input project.sdrf.tsv --database database.fasta
+   nextflow run nf-core/quantms -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input project.sdrf.tsv --database database.fasta --outdir <OUTDIR>
    ```
 
 ## Documentation

diff --git a/conf/dev.config b/conf/dev.config
@@ -1,11 +1,15 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running with nightly dev containers
- * -------------------------------------------------
- * Only overwrites the container. See dev/ folder for building instructions.
- * Use as follows:
- *   nextflow run nf-core/quantms -profile dev,<docker/singularity>
- */
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running with nightly dev. containers (mainly for OpenMS)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Only overwrites the container. E.g. uses the OpenMS nightly executable and thirdparty
+    containers. TODO Currently does nothing, we need to set it up.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test,<docker/singularity> [--outdir <OUTDIR>]
+
+-------------------------------------------------------------------------------------------
+*/
 
 params {
     config_profile_name = 'Development profile'

diff --git a/conf/test.config b/conf/test.config
@@ -1,24 +1,26 @@
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests (ISO)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/quantms -profile test,<docker/singularity>
+        nextflow run nf-core/quantms -profile test,<docker/singularity> [--outdir <OUTDIR>]
 
-----------------------------------------------------------------------------------------
+-------------------------------------------------------------------------------------------
 */
 
 params {
-    config_profile_name        = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name        = 'Test profile DDA ISO'
+    config_profile_description = 'Minimal test dataset to check pipeline function of the isotopic labelling branch of the pipeline'
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus   = 2
     max_memory = '6.GB'
     max_time   = '6.h'
 
+    outdir = "./results_iso"
+
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv'
 

diff --git a/conf/test_dia.config b/conf/test_dia.config
@@ -1,20 +1,26 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/quantms -profile test,<docker/singularity/podman>
- */
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests (DIA)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple test.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test_dia,<docker/singularity> [--outdir <OUTDIR>]
+
+------------------------------------------------------------------------------------------------
+*/
 
 params {
-    config_profile_name = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name        = 'Test profile for DIA'
+    config_profile_description = 'Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.'
+
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = 6.GB
     max_time = 48.h
 
+    outdir = './results_dia'
+
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci/PXD026600/PXD026600.sdrf.tsv'
     database = 'ftp://massive.ucsd.edu/MSV000087597/sequence/REF_EColi_K12_UPS1_combined.fasta'

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -5,14 +5,16 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf-core/quantms -profile test_full,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/quantms -profile test_full,<docker/singularity> [--outdir <OUTDIR>]
 
 ----------------------------------------------------------------------------------------
 */
 
 params {
-    config_profile_name        = 'Full test profile'
-    config_profile_description = 'Full test dataset to check pipeline function and sanity of results'
+    config_profile_name        = 'Full test profile DDA ISO'
+    config_profile_description = 'Full test dataset in isotopic labelling mode to check pipeline function and sanity of results'
+
+    outdir = "./results_iso_full"
 
     // Input data for full size test
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv'

diff --git a/conf/test_lfq.config b/conf/test_lfq.config
@@ -1,20 +1,26 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/quantms -profile test,<docker/singularity/podman>
- */
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests (LFQ)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple test.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test_lfq,<docker/singularity> [--outdir <OUTDIR>]
+
+------------------------------------------------------------------------------------------------
+*/
 
 params {
-    config_profile_name = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name        = 'Test profile for DDA LFQ'
+    config_profile_description = 'Minimal test dataset to check pipeline function of the label-free quantification branch of the pipeline'
+
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = 6.GB
     max_time = 48.h
 
+    outdir = "./results_lfq"
+
     // Input data
     labelling_type = "label free sample"
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci/BSA/BSA_design_urls.tsv'

diff --git a/conf/test_localize.config b/conf/test_localize.config
@@ -1,22 +1,26 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running tests with
- *  modification localization
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/quantms -profile test_localize,<docker/singularity/podman>
- */
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests (LFQ) with mod. localization
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple test.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test_localize,<docker/singularity> [--outdir <OUTDIR>]
+
+----------------------------------------------------------------------------------------------------
+*/
 
 params {
-    config_profile_name = 'Test phospho-localization profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function for phospho-localization, SDRF parsing and ConsensusID.'
+    config_profile_name        = 'Test PTM-localization profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function for PTM-localization, SDRF parsing and ConsensusID.'
 
     // Limit resources so that this can run on Travis
     max_cpus = 2
     max_memory = 6.GB
     max_time = 1.h
 
+    outdir = "./results_localize"
+
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/phospho/test_phospho.sdrf'
     database = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci_phospho/pools_crap_targetdecoy.fasta'

diff --git a/modules/local/librarygeneration/meta.yml b/modules/local/librarygeneration/meta.yml
@@ -45,4 +45,4 @@ output:
       description: File containing software version
       pattern: "*.{version.txt}"
 authors:
-  - "@Chengxin Dai"
+  - "@daichengxin"
diff --git a/modules/local/openms/consensusid/main.nf b/modules/local/openms/consensusid/main.nf
@@ -2,6 +2,7 @@ process CONSENSUSID {
     label 'process_medium'
     // TODO could be easily parallelized
     label 'process_single_thread'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

diff --git a/modules/local/openms/decoydatabase/main.nf b/modules/local/openms/decoydatabase/main.nf
@@ -1,5 +1,7 @@
 process DECOYDATABASE {
     label 'process_very_low'
+    label 'openms'
+
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :

diff --git a/modules/local/openms/epifany/main.nf b/modules/local/openms/epifany/main.nf
@@ -1,6 +1,8 @@
 process EPIFANY {
     label 'process_medium'
-    publishDir "${params.outdir}",
+    label 'openms'
+
+    publishDir "${params.outdir}"
 
     conda (params.enable_conda ? "bioconda::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

diff --git a/modules/local/openms/extractpsmfeatures/main.nf b/modules/local/openms/extractpsmfeatures/main.nf
@@ -1,6 +1,7 @@
 process EXTRACTPSMFEATURES {
     label 'process_very_low'
     label 'process_single_thread'
+    label 'openms'
 
     conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2=2020_04_03 bioconda::msgf_plus=2021.03.22 bioconda::openms=2.8.0 bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1 bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 bioconda::openms-thirdparty=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

diff --git a/modules/local/openms/falsediscoveryrate/main.nf b/modules/local/openms/falsediscoveryrate/main.nf
@@ -1,6 +1,7 @@
 process FALSEDISCOVERYRATE {
-    label 'process_very_low'
+    label 'process_low'
     label 'process_single_thread'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

diff --git a/modules/local/openms/filemerge/main.nf b/modules/local/openms/filemerge/main.nf
@@ -1,6 +1,7 @@
 process FILEMERGE {
     label 'process_medium'
     label 'process_single_thread'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

diff --git a/modules/local/openms/idconflictresolver/main.nf b/modules/local/openms/idconflictresolver/main.nf
@@ -1,5 +1,6 @@
 process IDCONFLICTRESOLVER {
     label 'process_low'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

diff --git a/modules/local/openms/idfilter/main.nf b/modules/local/openms/idfilter/main.nf
@@ -1,6 +1,9 @@
 process IDFILTER {
+    tag "$meta.id"
+
     label 'process_very_low'
     label 'process_single_thread'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

diff --git a/modules/local/openms/idmapper/main.nf b/modules/local/openms/idmapper/main.nf
@@ -1,6 +1,8 @@
 process IDMAPPER {
     tag "$meta.id"
+
     label 'process_medium'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?