Replace 1.4 for 1.0 in docs. Fixes nf-core#85

docs/configuration/adding_your_own.md

@@ -51,7 +51,7 @@ nextflow run nf-core/rnaseq -profile docker --reads '<path to your reads>' --fas
 
 Nextflow will recognise `nf-core/rnaseq` and download the pipeline from GitHub. The `-profile docker` configuration lists the [nfcore/rnaseq](https://hub.docker.com/r/nfcore/rnaseq/) image that we have created and is hosted at dockerhub, and this is downloaded.
 
-The public docker images are tagged with the same version numbers as the code, which you can use to ensure reproducibility. When running the pipeline, specify the pipeline version with `-r`, for example `-r v1.4`. This uses pipeline code and docker image from this tagged version.
+The public docker images are tagged with the same version numbers as the code, which you can use to ensure reproducibility. When running the pipeline, specify the pipeline version with `-r`, for example `-r 1.0`. This uses pipeline code and docker image from this tagged version.
 
 To add docker support to your own config file (instead of using the `docker` profile, which runs locally), add the following:
 
@@ -91,17 +91,17 @@ If you intend to run the pipeline offline, nextflow will not be able to automati
 First, pull the image file where you have an internet connection:
 
 > NB: The "tag" at the end of this command corresponds to the pipeline version.
-> Here, we're pulling the docker image for version 1.4 of the nfcore/rnaseq pipeline
+> Here, we're pulling the docker image for version 1.0 of the nfcore/rnaseq pipeline
 > Make sure that this tag corresponds to the version of the pipeline that you're using
 
 ```bash
-singularity pull --name nfcore-rnaseq-1.4.img docker://nfcore/rnaseq:1.4
+singularity pull --name nfcore-rnaseq-1.0.img docker://nfcore/rnaseq:1.0
 ```
 
 Then transfer this file and run the pipeline with this path:
 
 ```bash
-nextflow run /path/to/nfcore-rnaseq -with-singularity /path/to/nfcore-rnaseq-1.4.img
+nextflow run /path/to/nfcore-rnaseq -with-singularity /path/to/nfcore-rnaseq-1.0.img
 ```
 
 ### Bioconda

docs/configuration/local.md

@@ -19,7 +19,7 @@ Nextflow will recognise `nf-core/rnaseq` and download the pipeline from GitHub.
 For more information about how to work with reference genomes, see [`docs/configuration/reference_genomes.md`](docs/configuration/reference_genomes.md).
 
 ### Pipeline versions
-The public docker images are tagged with the same version numbers as the code, which you can use to ensure reproducibility. When running the pipeline, specify the pipeline version with `-r`, for example `-r v1.4`. This uses pipeline code and docker image from this tagged version.
+The public docker images are tagged with the same version numbers as the code, which you can use to ensure reproducibility. When running the pipeline, specify the pipeline version with `-r`, for example `-r 1.0`. This uses pipeline code and docker image from this tagged version.
 
 
 ## Singularity image
@@ -32,15 +32,15 @@ If you intend to run the pipeline offline, nextflow will not be able to automati
 First, pull the image file where you have an internet connection:
 
 > NB: The "tag" at the end of this command corresponds to the pipeline version.
-> Here, we're pulling the docker image for version 1.4 of the nfcore/rnaseq pipeline
+> Here, we're pulling the docker image for version 1.0 of the nfcore/rnaseq pipeline
 > Make sure that this tag corresponds to the version of the pipeline that you're using
 
 ```bash
-singularity pull --name nfcore-rnaseq-1.4.img docker://nfcore/rnaseq:1.4
+singularity pull --name nfcore-rnaseq-1.0.img docker://nfcore/rnaseq:1.0
 ```
 
 Then transfer this file and run the pipeline with this path:
 
 ```bash
-nextflow run /path/to/nfcore-rnaseq -with-singularity /path/to/nfcore-rnaseq-1.4.img
+nextflow run /path/to/nfcore-rnaseq -with-singularity /path/to/nfcore-rnaseq-1.0.img
 ```

docs/configuration/uppmax.md

@@ -20,11 +20,11 @@ First, to generate the singularity image, run the following command. Note that y
 First, pull the image file where you have an internet connection:
 
 > NB: The "tag" at the end of this command corresponds to the pipeline version.
-> Here, we're pulling the docker image for version 1.4 of the nfcore/rnaseq pipeline
+> Here, we're pulling the docker image for version 1.0 of the nfcore/rnaseq pipeline
 > Make sure that this tag corresponds to the version of the pipeline that you're using
 
 ```bash
-singularity pull --name nfcore-rnaseq-1.4.img docker://nfcore/rnaseq:1.4
+singularity pull --name nfcore-rnaseq-1.0.img docker://nfcore/rnaseq:1.0
 pwd # Prints path to your singularity container
 ```
 
@@ -35,9 +35,9 @@ or `.tar.gz` file). Once transferred, extract the pipeline files.
 For example, with a `.zip` file:
 
 ```bash
-unzip 1.4.zip
-mv rnaseq-1.4 nfcore-rnaseq # rename the folder
-cd nfcore-rnaseq
+unzip 1.0.zip
+mv nfcore-rnaseq-1.0 nfcore-rnaseq # rename the folder
+cd nfcore-rnaseq-1.0
 pwd # Prints full path to your pipeline
 ```
 
@@ -46,12 +46,12 @@ and execute Nextflow with the path to the pipeline, as so:
 
 ```bash
 cd /path/to/my/data/analysis
-nextflow run /path/to/nfcore-rnaseq -with-singularity /path/to/singularity/nfcore-rnaseq-1.4.img
+nextflow run /path/to/nfcore-rnaseq-1.0 -with-singularity /path/to/singularity/nfcore-rnaseq-1.0.img
 ```
 
 (Note that you'll need the other common flags such as `--reads` and `--genome` in addition to this command).
 
-> NB: Note that you should _not_ use the `-r 1.4` flag recommended elsewhere. This tells Nextflow to download
+> NB: Note that you should _not_ use the `-r 1.0` flag recommended elsewhere. This tells Nextflow to download
 > that version of the code when it runs. Here, you have already downloaded the code, so it generates an error.
 
 

docs/usage.md

@@ -36,7 +36,7 @@ nextflow pull nf-core/rnaseq
 ### Reproducibility
 It's a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
-First, go to the [nfcore/rnaseq releases page](https://github.com/nf-core/rnaseq/releases) and find the latest version number - numeric only (eg. `1.4`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.4`.
+First, go to the [nfcore/rnaseq releases page](https://github.com/nf-core/rnaseq/releases) and find the latest version number - numeric only (eg. `1.0`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.0`.
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
 
@@ -110,8 +110,6 @@ params {
 }
 ```
 
-> **NB:** Before v1.4 of the pipeline, the UPPMAX profile ran in reverse stranded mode by default. This was removed in the v1.4 release, so all profiles now run in unstranded mode by default.
-
 If you have a default strandedness set in your personal config file you can use `--unstranded` to overwrite it for a given run.
 
 These flags affect the commands used for several steps in the pipeline - namely HISAT2, featureCounts, RSeQC (`RPKM_saturation.py`) and StringTie: