Merge pull request #744 from jfy133/docs-improvement

Docs improvement

Author: jfy133

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 - [#723](https://github.com/nf-core/eager/issues/723) - Fixes empty fields in TSV resulting in uninformative error
 - Updated template to nf-core/tools 1.14
+- [#688](https://github.com/nf-core/eager/issues/688) - Clarified the pipeline is not just for humans and microbes, but also plants and animals, and also for modern DNA
 
 ### `Dependencies`
 
@@ -23,12 +24,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
-- [#729](https://github.com/nf-core/eager/issues/729) Added Bowtie2 flag `--maxins` for PE mapping modern DNA mapping contexts
+- [#729](https://github.com/nf-core/eager/issues/729) - Added Bowtie2 flag `--maxins` for PE mapping modern DNA mapping contexts
 
 ### `Fixed`
 
 - Corrected explanation of the "--min_adap_overlap" parameter for AdapterRemoval in the docs
-- [#725](https://github.com/nf-core/eager/pull/725) `bwa_index` doc update
+- [#725](https://github.com/nf-core/eager/pull/725) - `bwa_index` doc update
 - Re-adds gzip piping to AdapterRemovalFixPrefix to speed up process after reports of being very slow
 - Updated DamageProfiler citation from bioRxiv to publication
 

README.md

@@ -17,7 +17,7 @@
 ## Introduction
 
 <!-- nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
-**nf-core/eager** is a bioinformatics best-practise analysis pipeline for NGS sequencing based ancient DNA (aDNA) data analysis.
+**nf-core/eager** is a scalable and reproducible bioinformatics best-practise processing pipeline for genomic NGS sequencing data, with a focus on ancient DNA (aDNA) data. It is ideal for the (palaeo)genomic analysis of humans, animals, plants, microbes and even microbiomes.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. The pipeline pre-processes raw data from FASTQ inputs, or preprocessed BAM inputs. It can align reads and performs extensive general NGS and aDNA specific quality-control on the results. It comes with docker, singularity or conda containers making installation trivial and results highly reproducible.
 

docs/usage.md

@@ -930,11 +930,11 @@ can use yourself, or upload alongside your publication for others to use.
 To use the profile you just need to specify the file containing the profile you
 wish to use, and then the profile itself.
 
-For example, Aida (Andrades Valtueña) on her cluster `sdag` at the MPI-SHH
-(`shh`) in Jena could run the following:
+For example, Aida (Andrades Valtueña) at the MPI-SHH (`shh`) in Jena could run
+the following:
 
 ```bash
-nextflow run nf-core/eager -c /<path>/<to>/AndradesValtuena2018.config -profile shh,sdag,AndradesValtuena2018 --input '/<path>/<to>/<some_input>/' <...>
+nextflow run nf-core/eager -c /<path>/<to>/AndradesValtuena2018.config -profile shh,AndradesValtuena2018 --input '/<path>/<to>/<some_input>/' <...>
 ```
 
 Then a colleague at a different institution, such as the SciLifeLab, could run
@@ -1026,16 +1026,16 @@ running.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 <...>
 ```
 
 For the `-profile` parameter, I have indicated that I wish to use Singularity as
 my software container environment, and I will use the MPI-SHH institutional
 config as listed on
-[nf-core/configs](https://github.com/nf-core/configs/blob/master/conf/shh.config),
- using the profile for the 'sdag' cluster. These profiles specify settings
+[nf-core/configs](https://github.com/nf-core/configs/blob/master/conf/shh.config).
+These profiles specify settings
 optimised for the specific cluster/institution, such as maximum memory available
 or which scheduler queues to submit to. More explanations about configs and
 profiles can be seen in the [nf-core
@@ -1090,7 +1090,7 @@ FASTA file and the corresponding indices.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/hs37d5.fa' \
@@ -1115,7 +1115,7 @@ directory (which contains 'intermediate' working files and directories).
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \`
 --fasta '../Reference/genome/hs37d5.fa' \
@@ -1144,7 +1144,7 @@ string to be clipped.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/hs37d5.fa' \
@@ -1169,7 +1169,7 @@ with `--dedupper`.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/hs37d5.fa' \
@@ -1194,7 +1194,7 @@ and the reference.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/hs37d5.fa' \
@@ -1221,7 +1221,7 @@ unmapped reads.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/hs37d5.fa' \
@@ -1251,7 +1251,7 @@ fragment. We will therefore use `--bamutils_clip_half_udg_left` and
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/hs37d5.fa' \
@@ -1287,7 +1287,7 @@ you can download the file from [here](https://github.com/nf-core/test-datasets/b
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/hs37d5.fa' \
@@ -1321,7 +1321,7 @@ is simply named 'X'.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/hs37d5.fa' \
@@ -1362,7 +1362,7 @@ providing the name of the mitochondrial DNA contig in our reference genome with
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/hs37d5.fa' \
@@ -1404,7 +1404,7 @@ file of these sites that is specified with `--pileupcaller_snpfile`.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/hs37d5.fa' \
@@ -1646,16 +1646,16 @@ running.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_screening20200720' \
 <...>
 ```
 
 For the `-profile` parameter, I have indicated that I wish to use Singularity as
 my software container environment, and I will use the MPI-SHH institutional
 config as listed on
-[nf-core/configs](https://github.com/nf-core/configs/blob/master/conf/shh.config),
-and using the profile for the 'sdag' cluster. These profiles specify settings
+[nf-core/configs](https://github.com/nf-core/configs/blob/master/conf/shh.config).
+These profiles specify settings
 optimised for the specific cluster/institution, such as maximum memory available
 or which scheduler queues to submit to. More explanations about configs and
 profiles can be seen in the [nf-core
@@ -1710,7 +1710,7 @@ FASTA file and the corresponding indices.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_screening20200720' \
 --input 'screening20200720.tsv' \
 --fasta '../Reference/genome/GRCh38.fa' \
@@ -1735,7 +1735,7 @@ directory (which contains 'intermediate' working files and directories).
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_screening20200720' \
 --input 'screening20200720.tsv' \
 --fasta '../Reference/genome/GRCh38.fa' \
@@ -1764,7 +1764,7 @@ string to be clipped.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_screening20200720' \
 --input 'screening20200720.tsv' \
 --fasta '../Reference/genome/GRCh38.fa' \
@@ -1785,7 +1785,7 @@ tell nf-core/eager what to do with the off target reads from the mapping.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_screening20200720' \
 --input 'screening20200720.tsv' \
 --fasta '../Reference/genome/GRCh38.fa' \
@@ -1815,7 +1815,7 @@ documentation describing each parameters can be seen in the usage
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_screening20200720' \
 --input 'screening20200720.tsv' \
 --fasta '../Reference/genome/GRCh38.fa' \
@@ -1842,7 +1842,7 @@ have indicators of true aDNA, we will run 'maltExtract' of the
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_screening20200720' \
 --input 'screening20200720.tsv' \
 --fasta '../Reference/genome/GRCh38.fa' \
@@ -2113,16 +2113,16 @@ running.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 <...>
 ```
 
 For the `-profile` parameter, I have indicated that I wish to use Singularity as
 my software container environment, and I will use the MPI-SHH institutional
 config as listed on
-[nf-core/configs](https://github.com/nf-core/configs/blob/master/conf/shh.config),
-and using the profile for the 'sdag' cluster. These profiles specify settings
+[nf-core/configs](https://github.com/nf-core/configs/blob/master/conf/shh.config).
+These profiles specify settings
 optimised for the specific cluster/institution, such as maximum memory available
 or which scheduler queues to submit to. More explanations about configs and
 profiles can be seen in the [nf-core
@@ -2174,7 +2174,7 @@ FASTA file and the corresponding indices.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.fa' \
@@ -2199,7 +2199,7 @@ directory (which contains 'intermediate' working files and directories).
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.fa' \
@@ -2228,7 +2228,7 @@ the default minimum length of a poly-G string to be clipped.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.fa' \
@@ -2252,7 +2252,7 @@ will do this with `--bwaalnn` and `--bwaalnl` respectively.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.fa' \
@@ -2276,7 +2276,7 @@ hard-drive footprint.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.fa' \
@@ -2306,7 +2306,7 @@ clarity.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.fa' \
@@ -2337,7 +2337,7 @@ often a custom BED file with just genes of interest is recommended. Furthermore
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.fa' \
@@ -2375,7 +2375,7 @@ we do BAM trimming instead here as another demonstration of functionality.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.fa' \
@@ -2416,7 +2416,7 @@ need to specify that we want to use the trimmed bams from the previous step.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.fa' \
@@ -2459,7 +2459,7 @@ same settings and reference genome. We can do this as follows.
 ```bash
 nextflow run nf-core/eager \
 -r 2.2.0 \
--profile singularity,shh,sdag \
+-profile singularity,shh \
 -name 'projectX_preprocessing20200727' \
 --input 'preprocessing20200727.tsv' \
 --fasta '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.fa' \