setting snpeff directory name to lowercase in tower.yml

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - [#1502](https://github.com/nf-core/sarek/pull/1502) - export CNVs into VCF format in `bam_variant_calling_cnvkit`
+- [#1534](https://github.com/nf-core/sarek/pull/1534) - Handling `.fastq.gz.spring` files as input
 
 ### Changed
 
@@ -27,12 +28,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [#1572](https://github.com/nf-core/sarek/pull/1572) - correct tower.yml snpeff report path
 - [#1536](https://github.com/nf-core/sarek/pull/1536) - Correct typo `Strelka2` to `Strelka`
 - [#1541](https://github.com/nf-core/sarek/pull/1541) - Getting bam and bai published in the same folder
 - [#1542](https://github.com/nf-core/sarek/pull/1542) - Removing legacy configs of `CUSTOM_DUMPSOFTWAREVERSIONS`
 - [#1547](https://github.com/nf-core/sarek/pull/1547) - Correct typo in help text in nextflow_schema.json
 - [#1556](https://github.com/nf-core/sarek/pull/1556) - Fix display of some commands in `docs/usage.md`
 - [#1563](https://github.com/nf-core/sarek/pull/1563) - Fix `vep_cache_path_full` so that `--refseq/--merged` will work for ENSEMBLVEP
+- [#1570](https://github.com/nf-core/sarek/pull/1570) - Remove duplicated notes in FASTQC output docs
 
 ### Removed
 

assets/schema_input.json

@@ -47,17 +47,20 @@
                 "pattern": "^\\S+$",
                 "unique": ["patient", "sample"],
                 "anyOf": [
+                    {
+                        "dependentRequired": ["bam"]
+                    },
                     {
                         "dependentRequired": ["fastq_1"]
                     },
                     {
-                        "dependentRequired": ["bam"]
+                        "dependentRequired": ["spring_1"]
                     }
                 ],
                 "meta": ["lane"]
             },
             "fastq_1": {
-                "errorMessage": "FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
+                "errorMessage": "Gzipped FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
                 "anyOf": [
                     {
                         "type": "string",
@@ -72,7 +75,7 @@
                 "exists": true
             },
             "fastq_2": {
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
+                "errorMessage": "Gzipped FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
                 "dependentRequired": ["fastq_1"],
                 "anyOf": [
                     {
@@ -87,6 +90,37 @@
                 "format": "file-path",
                 "exists": true
             },
+            "spring_1": {
+                "errorMessage": "Gzipped and spring-compressed FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz.spring' or '.fastq.gz.spring'",
+                "anyOf": [
+                    {
+                        "type": "string",
+                        "pattern": "^\\S+\\.f(ast)?q\\.gz.spring$"
+                    },
+                    {
+                        "type": "string",
+                        "maxLength": 0
+                    }
+                ],
+                "format": "file-path",
+                "exists": true
+            },
+            "spring_2": {
+                "errorMessage": "Gzipped and spring-compressed FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz.spring' or '.fastq.gz.spring'",
+                "dependentRequired": ["spring_1"],
+                "anyOf": [
+                    {
+                        "type": "string",
+                        "pattern": "^\\S+\\.f(ast)?q\\.gz.spring$"
+                    },
+                    {
+                        "type": "string",
+                        "maxLength": 0
+                    }
+                ],
+                "format": "file-path",
+                "exists": true
+            },
             "table": {
                 "errorMessage": "Recalibration table cannot contain spaces and must have extension '.table'",
                 "anyOf": [

conf/modules/modules.config

@@ -50,6 +50,13 @@ process {
         ]
     }
 
+    withName: 'NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_.*' {
+        ext.prefix = { "${spring.simpleName}" }
+        publishDir       = [
+            enabled: false
+        ]
+    }
+
     withName: 'MOSDEPTH' {
         ext.args   = { !params.wes ? "-n --fast-mode --by 500" : ""}
         ext.prefix = {

conf/test/alignment_from_everything.config

@@ -0,0 +1,15 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/sarek -profile test,<extra_test_profile>,<docker/singularity> --outdir <OUTDIR>
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params {
+    input = "${projectDir}/tests/csv/3.0/bam_and_fastq_and_spring.csv"
+    tools = null
+}

docs/output.md

@@ -924,18 +924,17 @@ The plots display:
 <details markdown="1">
 <summary>Output files for all samples</summary>
 
-:::note
-The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
-:::
 **Output directory: `{outdir}/reports/fastqc/<sample-lane>`**
 
 - `<sample-lane_1>_fastqc.html` and `<sample-lane_2>_fastqc.html`
   - [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) report containing quality metrics for your untrimmed raw FastQ files
 - `<sample-lane_1>_fastqc.zip` and `<sample-lane_2>_fastqc.zip`
   - Zip archive containing the [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) report, tab-delimited data file and plot images
 
-> **NB:** The FastQC plots displayed in the [MultiQC](https://multiqc.info/) report shows _untrimmed_ reads.
-> They may contain adapter sequence and potentially regions with low quality.
+:::note
+The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads.
+They may contain adapter sequence and potentially regions with low quality.
+:::
 
 </details>
 

docs/usage.md

@@ -80,27 +80,29 @@ Output from Variant Calling and/or Annotation will be in a specific directory fo
 
 ### Overview: Samplesheet Columns
 
-| Column    | Description                                                                                                                                                                                                                                                                                                                       |
-| --------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `patient` | **Custom patient ID**; designates the patient/subject; must be unique for each patient, but one patient can have multiple samples (e.g. normal and tumor). <br /> _Required_                                                                                                                                                      |
-| `sex`     | **Sex chromosomes of the patient**; i.e. XX, XY..., only used for Copy-Number Variation analysis in a tumor/pair<br /> _Optional, Default: `NA`_                                                                                                                                                                                  |
-| `status`  | **Normal/tumor status of sample**; can be `0` (normal) or `1` (tumor).<br /> _Optional, Default: `0`_                                                                                                                                                                                                                             |
-| `sample`  | **Custom sample ID** for each tumor and normal sample; more than one tumor sample for each subject is possible, i.e. a tumor and a relapse; samples can have multiple lanes for which the _same_ ID must be used to merge them later (see also `lane`). Sample IDs must be unique for unique biological samples <br /> _Required_ |
-| `lane`    | Lane ID, used when the `sample` is multiplexed on several lanes. Must be unique for each lane in the same sample (but does not need to be the original lane name), and must contain at least one character <br /> _Required for `--step mapping`_                                                                                 |
-| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension `.fastq.gz` or `.fq.gz`.                                                                                                                                                                                                        |
-| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension `.fastq.gz` or `.fq.gz`.                                                                                                                                                                                                        |
-| `bam`     | Full path to (u)BAM file                                                                                                                                                                                                                                                                                                          |
-| `bai`     | Full path to BAM index file                                                                                                                                                                                                                                                                                                       |
-| `cram`    | Full path to CRAM file                                                                                                                                                                                                                                                                                                            |
-| `crai`    | Full path to CRAM index file                                                                                                                                                                                                                                                                                                      |
-| `table`   | Full path to recalibration table file                                                                                                                                                                                                                                                                                             |
-| `vcf`     | Full path to vcf file                                                                                                                                                                                                                                                                                                             |
+| Column     | Description                                                                                                                                                                                                                                                                                                                       |
+| ---------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `patient`  | **Custom patient ID**; designates the patient/subject; must be unique for each patient, but one patient can have multiple samples (e.g. normal and tumor). <br /> _Required_                                                                                                                                                      |
+| `sex`      | **Sex chromosomes of the patient**; i.e. XX, XY..., only used for Copy-Number Variation analysis in a tumor/pair<br /> _Optional, Default: `NA`_                                                                                                                                                                                  |
+| `status`   | **Normal/tumor status of sample**; can be `0` (normal) or `1` (tumor).<br /> _Optional, Default: `0`_                                                                                                                                                                                                                             |
+| `sample`   | **Custom sample ID** for each tumor and normal sample; more than one tumor sample for each subject is possible, i.e. a tumor and a relapse; samples can have multiple lanes for which the _same_ ID must be used to merge them later (see also `lane`). Sample IDs must be unique for unique biological samples <br /> _Required_ |
+| `lane`     | Lane ID, used when the `sample` is multiplexed on several lanes. Must be unique for each lane in the same sample (but does not need to be the original lane name), and must contain at least one character <br /> _Required for `--step mapping`_                                                                                 |
+| `fastq_1`  | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension `.fastq.gz` or `.fq.gz`.                                                                                                                                                                                                        |
+| `fastq_2`  | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension `.fastq.gz` or `.fq.gz`.                                                                                                                                                                                                        |
+| `spring_1` | Full path to spring-compressed, gzipped FastQ file for read 1 or for reads 1 and 2. The Fastq file has to be first gzipped, then spring-compressed, and it must have the extension `.fastq.gz` or `.fq.gz`.                                                                                                                       |
+| `spring_2` | Full path to spring-compressed, gzipped FastQ file for read 2. The Fastq file has to be first gzipped, then spring-compressed, and it must have the extension `.fastq.gz` or `.fq.gz`.                                                                                                                                            |
+| `bam`      | Full path to (u)BAM file                                                                                                                                                                                                                                                                                                          |
+| `bai`      | Full path to BAM index file                                                                                                                                                                                                                                                                                                       |
+| `cram`     | Full path to CRAM file                                                                                                                                                                                                                                                                                                            |
+| `crai`     | Full path to CRAM index file                                                                                                                                                                                                                                                                                                      |
+| `table`    | Full path to recalibration table file                                                                                                                                                                                                                                                                                             |
+| `vcf`      | Full path to vcf file                                                                                                                                                                                                                                                                                                             |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
 ### Start with mapping (`--step mapping` [default])
 
-This step can be started either from FastQ files or (u)BAMs. The CSV must contain at least the columns `patient`, `sample`, `lane`, and either `fastq_1/fastq_2` or `bam`.
+This step can be started either from FastQ files (gzip-compressed or gzip+spring-compressed) or (u)BAMs. The CSV must contain at least the columns `patient`, `sample`, `lane`, and `fastq_1/fastq_2`, `spring_1`, `spring_1/spring_2` or `bam`.
 
 #### Examples
 
@@ -111,6 +113,16 @@ patient,sample,lane,fastq_1,fastq_2
 patient1,test_sample,lane_1,test_1.fastq.gz,test_2.fastq.gz
 ```
 
+```bash
+patient,sample,lane,spring_1
+patient1,test_sample,lane_1,test_R1_and_R2.fastq.gz.spring
+```
+
+```bash
+patient,sample,lane,spring_1,spring_2
+patient1,test_sample,lane_1,test_R1.fastq.gz.spring,test_R2.fastq.gz.spring
+```
+
 ```bash
 patient,sample,lane,bam
 patient1,test_sample,lane_1,test.bam

modules.json

@@ -449,6 +449,11 @@
                         "git_sha": "2f3db6f45147ebbb56b371536e31bdf622b5bfee",
                         "installed_by": ["modules", "vcf_annotate_snpeff"]
                     },
+                    "spring/decompress": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "strelka/germline": {
                         "branch": "master",
                         "git_sha": "e8f2c77a6e4174ee0a48d073d4cc8ff06c44bb4c",