add some docs

README.md

@@ -4,9 +4,7 @@ This Nextflow pipeline is intended for preprocessing of DNA-seq
 experiments such as ATAC-seq, ChIP-seq and CUT&RUN. It currently
 performs trimming and alignment of fastq files, filtering of the
 resulting BAM files, basic peak calling and a QC assessment by
-calculating Fractions Of Reads Per Peaks (FRiPs). Specific CUT&RUN
-features might be added in later versions, the defaults should work well
-for most input data though.
+calculating Fractions Of Reads Per Peaks (FRiPs). 
 
 <br>
 
@@ -20,31 +18,44 @@ for most input data though.
 
 ## Usage
 
-...documentation will follow...
+Creating an index for the mapping on our HPC, with 16 cores using SLURM and the `normal` queue.
+Output will be in `atac_chip_preprocess_results/bowtie2_idx/` created in the location from which the run is launched.
 
-## Citations
+```bash
 
--   [nf-core project](https://nf-co.re/)
+NXF_VER=21.04.3 \
+    nextflow run atpoint/atac_chip_preprocess -r 2.0 -profile singularity,slurm -with-trace -with-report report.html \
+        --ref_genome /path/to/genome.fa.gz --idx_threads 16 --idx_mem '16.GB' --only_idx --queue 'normal' \
+        -bg > report.log
 
--   [Ewels et al (2020) The nf-core paper. Nature Biotechnology volume
-    38, pages
-    276–278](https://www.nature.com/articles/s41587-020-0439-x)
+```
 
--   [Nextflow Docs](https://www.nextflow.io/docs/latest/index.html#)
+Mapping a dataset. Note, for single-end data use `--mode single`, for paired-end data use `--mode paired` and for ATAC-seq
+add additionally the `--atacseq` flag.
 
--   [Seqera Training](https://seqera.io/training/)
+```bash
 
--   [https://github.com/nextflow-io/rnaseq-nf -- The Seqera Labs DSL2
-    proof-of-concept workflow](https://github.com/nextflow-io/rnaseq-nf)
+NXF_VER=21.04.3 \
+    nextflow run atpoint/atac_chip_preprocess -r 2.0 -profile singularity,slurm -with-trace -with-report report.html \
+        --idx path/to/idx/idxbasename \
+        --fastq "$(pwd)"'/*_{1,2}.fastq.gz' \
+        --align_threads 12 --sort_threads 2 --sort_mem '4G' --queue 'normal' \
+        -bg > report.log
 
--   [Merkel, D (2014). Docker: lightweight linux containers for
-    consistent development and deployment. Linux
-    Journal](https://dl.acm.org/doi/10.5555/2600239.2600241)
+```
 
--   [Kurtzer et al (2017) Singularity: Scientific containers for
-    mobility of compute. PLoS
-    ONE](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177459)
+## Pipeline
+
+- trim reads with `cutadapt`, either the TruSeq adapter (default) or the Nextera adapter (default is using `--atacseq`)
+- map trimmed reads with `bowtie2` and mark duplicates with `samblaster`
+- remove unmapped reads, alignments with MAPQ < 20, mitochondrial alignments (for ATAC-seq), alignments to non-primary chromosomes,
+non-primary and supplementary alignments, PCR duplicates
+- call peaks per sample with `macs2`
+- calculate FRiPs per sample based on the per-sample peaks
+- check insert sizes (for paired-end data)
+
+## Containerization
+
+Use either `-profile docker,singularity` to run via the hardcoded container. 
+Using `-profile conda` is possible but untested, it will build the environment based on the `environment.yml` file which the container is based on.
 
--   [Grüning et al (2018) Bioconda: sustainable and comprehensive
-    software distribution for the life sciences. Nat Methods
-    15:475-476](https://www.nature.com/articles/s41592-018-0046-7)