Merge pull request #3 from nf-core/dev

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nf-core · Jun 27, 2019 · 7cb1a10 · 7cb1a10
2 parents 2fb6eff + 544c217
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diff --git a/README.md b/README.md
@@ -34,24 +34,12 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
         * reads where only one read of the pair fails the above criteria ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html); *paired-end only*)
     3. Alignment-level QC and estimation of library complexity ([`picard`](https://broadinstitute.github.io/picard/), [`Preseq`](http://smithlabresearch.org/software/preseq/))
     4. Create normalised bigWig files scaled to 1 million mapped reads ([`BEDTools`](https://github.com/arq5x/bedtools2/), [`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/))
-    5. Generate gene-body meta-profile from bigWig files ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html))
-    6. Calculate genome-wide coverage assessment ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html))
-    7. Call nucleosome positions and generate smoothed, normalised coverage wig files that can be used to generate occupancy profile plots between samples across features of interest ([`DANPOS2`](https://sites.google.com/site/danposdoc/))
-6. Create IGV session file containing bigWig tracks, peaks and differential sites for data visualisation ([`IGV`](https://software.broadinstitute.org/software/igv/)).
+    5. Calculate genome-wide coverage assessment ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html))
+    6. Call nucleosome positions and generate smoothed, normalised coverage bigWig files that can be used to generate occupancy profile plots between samples across features of interest ([`DANPOS2`](https://sites.google.com/site/danposdoc/))
+    7. Generate gene-body meta-profile from DANPOS2 smoothed bigWig files ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html))
+6. Create IGV session file containing bigWig tracks for data visualisation ([`IGV`](https://software.broadinstitute.org/software/igv/)).
 7. Present QC for raw read and alignment results ([`MultiQC`](http://multiqc.info/))
 
-## Documentation
-The nf-core/mnaseseq pipeline comes with documentation about the pipeline, found in the `docs/` directory:
-
-1. [Installation](https://nf-co.re/usage/installation)
-2. Pipeline configuration
-    * [Local installation](https://nf-co.re/usage/local_installation)
-    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)
-    * [Reference genomes](https://nf-co.re/usage/reference_genomes)
-3. [Running the pipeline](docs/usage.md)
-4. [Output and how to interpret the results](docs/output.md)
-5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
-
 ## Quick Start
 
 i. Install [`nextflow`](https://nf-co.re/usage/installation)
@@ -72,6 +60,18 @@ nextflow run nf-core/mnaseseq -profile <docker/singularity/conda> --design desig
 
 See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
 
+## Documentation
+The nf-core/mnaseseq pipeline comes with documentation about the pipeline, found in the `docs/` directory:
+
+1. [Installation](https://nf-co.re/usage/installation)
+2. Pipeline configuration
+    * [Local installation](https://nf-co.re/usage/local_installation)
+    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)
+    * [Reference genomes](https://nf-co.re/usage/reference_genomes)
+3. [Running the pipeline](docs/usage.md)
+4. [Output and how to interpret the results](docs/output.md)
+5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
+
 ## Credits
 
 The pipeline was originally written by the [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) for use at [The Francis Crick Institute](https://www.crick.ac.uk/), London.

diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
@@ -45,6 +45,11 @@ module_order:
         info: 'This section of the report shows SAMTools results after merging libraries and before filtering.'
         path_filters:
             - '*mLb.mkD.sorted.bam*'
+    - picard:
+        name: 'Picard (merged library; unfiltered)'
+        info: 'This section of the report shows picard results after merging libraries and before filtering.'
+        path_filters:
+            - '*mLb.mkD*'
     - preseq:
         name: 'Preseq (merged library; unfiltered)'
         info: 'This section of the report shows Preseq results after merging libraries and before filtering.'
@@ -59,7 +64,7 @@ module_order:
         name: 'Picard (merged library; filtered)'
         info: 'This section of the report shows picard results after merging libraries and after filtering.'
         path_filters:
-            - '*mLb*'
+            - '*mLb.clN*'
     - deeptools:
         name: 'deepTools'
         info: 'This section of the report shows QC plots generated by deepTools.'
@@ -76,3 +81,6 @@ custom_plot_config:
     picard-insertsize:
         cpswitch_c_active: False
         smooth_points: 1000
+    picard-insertsize-1:
+        cpswitch_c_active: False
+        smooth_points: 1000
diff --git a/assets/nfcore-mnaseseq_logo.png b/assets/nfcore-mnaseseq_logo.png
diff --git a/docs/images/igv_screenshot.png b/docs/images/igv_screenshot.png
diff --git a/docs/images/mqc_cutadapt_plot.png b/docs/images/mqc_cutadapt_plot.png
diff --git a/docs/images/mqc_deeptools_plotFingerprint_plot.png b/docs/images/mqc_deeptools_plotFingerprint_plot.png
diff --git a/docs/images/mqc_deeptools_plotProfile_plot.png b/docs/images/mqc_deeptools_plotProfile_plot.png
diff --git a/docs/images/mqc_picard_deduplication_plot.png b/docs/images/mqc_picard_deduplication_plot.png
diff --git a/docs/images/mqc_picard_insert_size_plot.png b/docs/images/mqc_picard_insert_size_plot.png
diff --git a/docs/images/mqc_preseq_plot.png b/docs/images/mqc_preseq_plot.png
diff --git a/docs/images/mqc_samtools_stats_plot.png b/docs/images/mqc_samtools_stats_plot.png
diff --git a/docs/output.md b/docs/output.md
@@ -100,7 +100,7 @@ The library-level alignments associated with the same sample are merged and subs
     * `bwa/mergedLibrary/samtools_stats/`  
       SAMtools `*.flagstat`, `*.idxstats` and `*.stats` files generated from the alignment files.
     * `bwa/mergedLibrary/picard_metrics/`  
-      Alignment QC files from picard CollectMultipleMetrics and the metrics file from MarkDuplicates: `*_metrics` and `*.metrics.txt`, respectively.
+      Alignment QC files from picard CollectMultipleMetrics and the metrics file from MarkDuplicates: `*_metrics` and `*.metrics.txt`, respectively. These are generated both *before* (`*.mLb.mkD.*`) and *after* (`*.mLb.clN.*`) read filtering.
     * `bwa/mergedLibrary/picard_metrics/pdf/`  
       Alignment QC plot files in `*.pdf` format from picard CollectMultipleMetrics.
     * `bwa/mergedLibrary/preseq/`  
@@ -128,15 +128,27 @@ The library-level alignments associated with the same sample are merged and subs
 
     ![MultiQC - deepTools plotFingerprint plot](images/mqc_deeptools_plotFingerprint_plot.png)  
 
-    The results from deepTools plotProfile gives you a quick visualisation for the genome-wide enrichment of your samples at the TSS, and across the gene body. During the downstream analysis, you may want to refine the features/genes used to generate these plots in order to see a more specific condition-related effect.
-
-    ![MultiQC - deepTools plotProfile plot](images/mqc_deeptools_plotProfile_plot.png)  
+    The results from deepTools plotProfile gives you a quick visualisation for the genome-wide enrichment of your samples at the TSS. During the downstream analysis, you may want to refine the features/genes used to generate these plots in order to see a more specific condition-related effect.
 
     *Output directories*:
     * `bwa/mergedLibrary/deepTools/plotFingerprint/`  
-      * Output files: `*.plotFingerprint.pdf`, `*.plotFingerprint.qcmetrics.txt`, `*.plotFingerprint.raw.txt`
+      `*.plotFingerprint.pdf`, `*.plotFingerprint.qcmetrics.txt`, `*.plotFingerprint.raw.txt`
     * `bwa/mergedLibrary/deepTools/plotProfile/`  
-      * Output files: `*.computeMatrix.mat.gz`, `*.computeMatrix.vals.mat.gz`, `*.plotProfile.pdf`, `*.plotProfile.tab`.
+      `*.computeMatrix.mat.gz`, `*.computeMatrix.vals.mat.gz`, `*.plotProfile.pdf`, `*.plotProfile.tab`.
+
+4. **Nucleosome profiling**
+
+    *Documentation*:  
+    [DANPOS2](https://sites.google.com/site/danposdoc/home/dpos)
+
+    *Description*:  
+    The DANPOS2 `dpos` tool is used by the pipeline in order to analyse the fuzziness and occupancy at each nucleosome. The tool generates a smoothed `bigWig` file normalised to 1 million reads that can also be used downstream by tools such as `deepTools` to plot average occupancy profiles across regions of interest.
+
+    *Output directories*:
+    * `bwa/mergedLibrary/danpos/`  
+      * Normalised and smoothed `*.bigWig` files scaled to 1 million reads.  
+      * `.xls` file containing nucleosome position information.  
+      * BED files containing nucleosome positions (`*.bed`) and summit information (`*.summit.bed`).  
 
 ## Aggregate analysis
 
@@ -148,7 +160,7 @@ The library-level alignments associated with the same sample are merged and subs
     *Description*:  
     MultiQC is a visualisation tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available within the report data directory.  
 
-    Results generated by MultiQC collate pipeline QC from FastQC, TrimGalore, samtools flagstat, samtools idxstats, samtools stats, picard CollectMultipleMetrics, picard MarkDuplicates, Preseq, deepTools plotProfile and deepTools plotFingerprint (see [`multiqc config file`](../assets/multiqc_config.yaml)).  
+    Results generated by MultiQC collate pipeline QC from FastQC, TrimGalore, samtools flagstat, samtools idxstats, samtools stats, picard CollectMultipleMetrics, picard MarkDuplicates, Preseq and deepTools plotFingerprint (see [`multiqc config file`](../assets/multiqc_config.yaml)).  
 
     The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
 
@@ -164,7 +176,7 @@ The library-level alignments associated with the same sample are merged and subs
     [IGV](https://software.broadinstitute.org/software/igv/UserGuide)
 
     *Description*:  
-    An IGV session file will be created at the end of the pipeline containing the normalised bigWig tracks. This avoids having to load all of the data individually into IGV for visualisation.
+    An IGV session file will be created at the end of the pipeline containing the normalised bigWig tracks (both smoothed and unsmoothed), nucleosome positions and associated summits. This avoids having to load all of the data individually into IGV for visualisation.
 
     The genome fasta file required for the IGV session will be the same as the one that was provided to the pipeline. This will be copied into `reference_genome/` to overcome any loading issues. If you prefer to use another path or an in-built genome provided by IGV just change the `genome` entry in the second-line of the session file.
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -31,6 +31,9 @@
   * [`--skipTrimming`](#--skiptrimming)
   * [`--saveTrimmed`](#--savetrimmed)
 * [Alignments](#alignments)
+  * [`--min_insert`](#--min_insert)
+  * [`--max_insert`](#--max_insert)
+  * [`--max_mismatch`](#--max_mismatch)
   * [`--keepDups`](#--keepdups)
   * [`--keepMultiMap`](#--keepmultimap)
   * [`--saveAlignedIntermediates`](#--savealignedintermediates)