Merge pull request #174 from nf-core/dev

Patch release

CHANGELOG.md

@@ -3,6 +3,15 @@
 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).
 
+## [v2.2.1 Romarin Curie - patch](https://github.com/nf-core/crisprseq/releases/tag/2.2.1) - [23.07.2024]
+
+### Fixed
+
+- Fix singularity image pull tag for MAGeCKFlute ([#160](https://github.com/nf-core/crisprseq/pull/160))
+- Escape dollar signs in `containerOptions` ([#163](https://github.com/nf-core/crisprseq/pull/163))
+- Fix error in R script when adding patterns ([#170](https://github.com/nf-core/crisprseq/pull/170))
+- Skip MAGeCKFlute when the function produces an error within the R package ([#171](https://github.com/nf-core/crisprseq/pull/170))
+
 ## [v2.2.0 - Romarin Curie](https://github.com/nf-core/crisprseq/releases/tag/2.2.0) - [20.06.2024]
 
 ### Added

README.md

@@ -79,18 +79,14 @@ For crispr screening:
 
 First, prepare a samplesheet with your input data that looks as follows:
 
-`samplesheet.csv`:
-
-```csv
+```csv title="samplesheet.csv"
 sample,fastq_1,fastq_2,reference,protospacer,template
 SAMPLE1,SAMPLE1_R1.fastq.gz,SAMPLE1_R2.fastq.gz,ACTG,ACTG,ACTG
 ```
 
 or
 
-`samplesheet.csv`:
-
-```csv
+```csv title="samplesheet.csv"
 sample,fastq_1,fastq_2,condition
 SAMPLE1,SAMPLE1_R1.fastq.gz,SAMPLE1_R2.fastq.gz,control
 ```

assets/multiqc_config.yml

@@ -1,8 +1,8 @@
 report_comment: >
 
-  This report has been generated by the <a href="https://github.com/nf-core/crisprseq/releases/tag/2.2.0" target="_blank">nf-core/crisprseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/crisprseq/releases/tag/2.2.1" target="_blank">nf-core/crisprseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/crisprseq/2.2.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/crisprseq/2.2.1/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-crisprseq-methods-description":

bin/cigar_parser.R

@@ -772,7 +772,7 @@ ref_fasta = opt$reference
 gRNA_sequence = opt$gRNA_sequence
 sample_id = opt$sample_name
 temp = opt$template
-spikes = opt$spikes ### yes or no
+spikes = opt$spikes
 files_summary = opt$summary_file
 cut_pos_prot = as.numeric(opt$cut_site)
 mock = opt$mock
@@ -900,6 +900,7 @@ if (dim(alignment_info)[1] != 0){
             separated_indels["post_ins_nt"]<-NA
         }else if(dim(separated_indels_ins_all)[1]>0){
             separated_indels <- separated_indels_ins_all
+            separated_indels["patterns"]<-NA
         }
 
 

docs/usage.md

@@ -52,7 +52,7 @@ nextflow run nf-core/crisprseq -profile docker -params-file params.yaml
 
 with `params.yaml` containing:
 
-```yaml
+```yaml title="params.yaml"
 input: './samplesheet.csv'
 outdir: './results/'
 genome: 'GRCh37'

docs/usage/screening.md

@@ -17,7 +17,7 @@ The **nf-core/crisprseq** pipeline allows the analysis of CRISPR edited CRISPR p
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/crisprseq --analysis screening --input samplesheet.csv --library library.csv --outdir <OUTDIR> -profile docker
+nextflow run nf-core/crisprseq --analysis screening --input samplesheet.csv --library library.tsv --outdir <OUTDIR> -profile docker
 ```
 
 The following required parameters are here described.
@@ -27,7 +27,7 @@ If you wish to input a raw count or normalized table, you can skip the sampleshe
 
 The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 4 columns to match those defined in the table below.
 
-```console
+```csv title="samplesheet.csv"
 sample,fastq_1,fastq_2,condition
 SRR8983579,SRR8983579.small.fastq.gz,,control
 SRR8983580,SRR8983580.small.fastq.gz,,treatment

docs/usage/targeted.md

@@ -24,7 +24,7 @@ You will need to create a samplesheet with information about the samples you wou
 
 The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes _(see section below for an explanation of samplesheet columns)_:
 
-```console
+```csv title="samplesheet.csv"
 sample,fastq_1,fastq_2,reference,protospacer,template
 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,GCT...CCT,GGGGCCACTAGGGACAGGAT,
 CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,GCT...CCT,GGGGCCACTAGGGACAGGAT,
@@ -37,7 +37,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th
 
 A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 3 samples, where `chr6` is single-end and has a template sequence _(this is a reduced samplesheet, please refer to the [pipeline example samplesheet](https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata-edition/samplesheet_test_full.csv) to see the full version)_.
 
-```console
+```csv title="samplesheet.csv"
 sample,fastq_1,fastq_2,reference,protospacer,template
 hCas9-TRAC-a,hCas9-TRAC-a_R1.fastq.gz,hCas9-TRAC-a_R2.fastq.gz,GCT...CCT,GGGGCCACTAGGGACAGGAT,
 hCas9-AAVS1-a,hCas9-AAVS1-a_R1.fastq.gz,hCas9-AAVS1-a_R2.fastq.gz,GCT...CCT,GGGGCCACTAGGGACAGGAT,
@@ -108,8 +108,7 @@ Please refer to the original [CRISPR-Analytics](https://doi.org/10.1371/journal.
 
 In order to customise such parameters, you can override the arguments given to `minimap2` by creating a configuration file and provide it to your nextflow run with `-c`:
 
-```groovy
-// Custom config file custom.config
+```groovy title="custom.config"
 process {
     withName: MINIMAP2_ALIGN_ORIGINAL {
         ext.args = '-A 29 -B 17 -O 25 -E 2'

modules/local/mageck/flutemle.nf

@@ -5,7 +5,7 @@ process MAGECK_FLUTEMLE {
 
     conda "bioconda::bioconductor-mageckflute=2.2.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mageckflute:2.2.0--r42hdfd78af_0':
+        'https://depot.galaxyproject.org/singularity/bioconductor-mageckflute:2.2.0--r42hdfd78af_0':
         'biocontainers/bioconductor-mageckflute:2.2.0--r42hdfd78af_0' }"
 
     input:

nextflow.config

@@ -140,10 +140,10 @@ profiles {
         shifter.enabled          = false
         charliecloud.enabled     = false
         apptainer.enabled        = false
-        process.containerOptions = '-u $(id -u):$(id -g)'
+        process.containerOptions = '-u \$(id -u):\$(id -g)'
     }
     arm {
-        process.containerOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        process.containerOptions = '-u \$(id -u):\$(id -g) --platform=linux/amd64'
     }
     singularity {
         singularity.enabled     = true
@@ -285,7 +285,7 @@ manifest {
     description     = """Pipeline for the analysis of CRISPR data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.2.0'
+    version         = '2.2.1'
     doi             = 'https://doi.org/10.5281/zenodo.7598496'
 }
 

templates/template_fluteMLE.R

@@ -17,14 +17,28 @@
         before_beta <- sub("\\\\.beta.*", "", beta_strings)
         unique_strings <- unique(before_beta)
         for(i in unique_strings) {
-            FluteMLE(mle, treatname= i, proj=i, pathview.top=5)
-            }
+            tryCatch(
+                {
+                    FluteMLE(mle, treatname= i, proj=i, pathview.top=5)
+                },
+            error=function(e) {
+                    print(paste("Could not run FluteMLE with project",i))
+                }
+            )
+        }
     } else {
         beta_strings <- grep("\\\\.beta", colnames(mle), value = TRUE)
         before_beta <- sub("\\\\.beta.*", "", beta_strings)
         unique_strings <- unique(before_beta)
         for(i in unique_strings) {
-            FluteMLE(mle, treatname= i, proj=i, ${args}, pathview.top=5)
+            tryCatch(
+                {
+                FluteMLE(mle, treatname= i, proj=i, ${args}, pathview.top=5)
+                },
+            error=function(e) {
+                    print(paste("Could not run FluteMLE with project",i))
+                }
+            )
         }
     }