Prepare release v1.0.8

README.md

@@ -31,13 +31,13 @@ Please cite [our paper](https://academic.oup.com/nargab/article/6/1/lqae015/7602
 2. Run the pipeline on a test dataset
 
 ```
-nextflow run genepi/nf-gwas -r v1.0.7 -profile test,<docker,singularity,slurm,slurm_with_scratch>
+nextflow run genepi/nf-gwas -r v1.0.8 -profile test,<docker,singularity,slurm,slurm_with_scratch>
 ```
 
 3. Run the pipeline on your data
 
 ```
-nextflow run genepi/nf-gwas -c <nextflow.config> -r v1.0.7 -profile <docker,singularity,slurm,slurm_with_scratch>
+nextflow run genepi/nf-gwas -c <nextflow.config> -r v1.0.8 -profile <docker,singularity,slurm,slurm_with_scratch>
 ```
 
 Please click [here](tests) for available test config files.

docs/configuration/profiles.md

@@ -9,7 +9,7 @@ nav_order: 3
 
 nf-gwas provides different execution profiles which can be specified with the `-profile` parameter.
 
-`nextflow run genepi/nf-gwas -r v1.0.0 -profile test, <docker,singularity,development, slurm,slurm_with_scratch>`.
+`nextflow run genepi/nf-gwas -r v1.X.X -profile test, <docker,singularity,development, slurm,slurm_with_scratch>`.
 
 ### Docker
 For local runs, [Docker](https://docs.docker.com/get-docker/) is the easiest way to run the pipeline.

docs/gwas-regenie-101/basic-tasks.md

@@ -6,7 +6,7 @@ nav_order: 3
 ---
 
 ## Mastering the basic tasks
-As mentioned in the beginning, I am working on a Windows computer, so I cannot run the pipeline locally. However, my institute has a Linux server on which Nextflow is installed. So the first steps for you are to 1) gain access to a server, a Linux computer that you can access remotely or a cluster and 2) ask the administrator to [install Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation) on it (Version ≥ 21.04.0).
+As mentioned in the beginning, I am working on a Windows computer, so I cannot run the pipeline locally. However, my institute has a Linux server on which Nextflow is installed. So the first steps for you are to 1) gain access to a server, a Linux computer that you can access remotely or a cluster and 2) ask the administrator to [install Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation) on it (Version ≥ 22.10.04).
 
 ### Accessing a remote server
 

docs/gwas-regenie-101/cmd-tools.md

@@ -12,6 +12,6 @@ nav_order: 6
 | `ls` | Will print all files and directories within your present working directory | If you put a path (absolute or relative) after `ls` it will print the content of this directory) e.g. `ls /home` will print the content of the folder home; If you add `-l` it will print the files and directories in a list that contains additional information such as permissions |
 | `mkdir` | Will make a new directory in your present working directory | `mkdir GWAS` will make a directory called `GWAS` |
 | `cd` | Change directories | If you only enter `cd` without an absolute or relative path, it will change to your home directory; Entering `cd ..` will change your current directory to the parent folder; Entering `cd` with an absolute or relative path will change the directory to the respective folder |
-| `nextflow run genepi/nf-gwas -c <nextflow.config> -r v1.0.0 –profile singularity` | Will run the gwas pipeline | Adding `-bg` will continue to run the pipeline even if you close the command line; Adding `-resume` will continue the pipeline with the files that have already been generated by a run of the same config file (e.g. if you only change the settings for the annotation files, it does not have to rerun the whole pipeline); Exchange `<nextflow.config>` with the name of your config file; Version of the pipeline is adapted simply by changing the version (`v1.0.0`); Instead of `singularity` also `docker`and `slurm` are currently available |
+| `nextflow run genepi/nf-gwas -c <nextflow.config> -r v1.X.X –profile singularity` | Will run the gwas pipeline | Adding `-bg` will continue to run the pipeline even if you close the command line; Adding `-resume` will continue the pipeline with the files that have already been generated by a run of the same config file (e.g. if you only change the settings for the annotation files, it does not have to rerun the whole pipeline); Exchange `<nextflow.config>` with the name of your config file; Version of the pipeline is adapted simply by changing the version (`v1.X.X`); Instead of `singularity` also `docker`and `slurm` are currently available |
 | `htop` | Will display the current processes that are running | Hit `q` to quit |
 | `vi` | A text editor in Linux that can display the content of a file, an alternative is for example `nano` (it can be used in the same way, but the advantage is that you can immediately start to modify the file) | E.g. enter `vi first-gwas.config` to view the content of the first-gwas.config file;To quit just type in the following command and hit enter `:q!`; After running a GWAS you might notice a `.nextflow.log` file in you folder when you check via FileZilla but you don't see them if you enter ls in the command line because the dot in the beginning of the file means its hidden. However, you can still look at the content of such a file by entering `vi .nextflow.log` |

docs/gwas-regenie-101/error-handling.md

@@ -8,7 +8,7 @@ nav_order: 4
 
 Before running the pipeline on your own data, you can run the pipeline with a small test dataset with the following command:
 ```
-nextflow run genepi/nf-gwas -r v1.0.0 -profile test,docker -bg
+nextflow run genepi/nf-gwas -r v1.X.X -profile test,docker -bg
 ```
 (adapt the -r and -profile to the one you want to use on your data; for this to work the container software - e.g. [docker](https://docs.docker.com/get-docker/) - must also be pre-installed)
 
@@ -18,7 +18,7 @@ If you still cannot find a solution, post an issue on the GitHub page, I am sure
 
 There are two errors I came across, that are not formatting problems of your input files. If you have the same ones, here are the solutions:
 
-- Error: `Cannot find revision 'v1.0.0'` -- Make sure that it exists in the remote repository `https://github.com/genepi/nf-gwas`
+- Error: `Cannot find revision 'v1.X.X'` -- Make sure that it exists in the remote repository `https://github.com/genepi/nf-gwas`
 -> This happens to me every time I use a new version of the pipeline. If the version exists on GitHub, just re-run the same command, then it works
 - Command error: `Failed to open --vcf file : Permission denied`
 -> of course this could also happen for other files, it means that you don't have reading permission for these files. In this case you have to ask the administrator to give you reading permissions for these files. You can also check the permissions for a file by navigating to the folder and entering the `ls -l` command (the `-l` will list the files in the directory and on the left side it will display the permissions for each file)

docs/gwas-regenie-101/run-pipeline.md

@@ -17,7 +17,7 @@ Useful tip: as indicated on the GitHub repository, the genotypes have to be a si
 
 To run the pipeline with the `first-gwas.config` configuration file, you simply change the working directory to the GWAS folder (`cd /home/myHome/GWAS`) and type in the following command:
 ```
-nextflow run genepi/nf-gwas -c first-gwas.config -r v1.0.0 -profile docker -bg
+nextflow run genepi/nf-gwas -c first-gwas.config -r v1.X.X -profile docker -bg
 ```
 In more detail:
 
@@ -27,7 +27,7 @@ In more detail:
 
 * `-c first-gwas.config` tells the pipeline which configuration file it should use (just exchange first-gwas.config with the name of your config file)
 
-* `-r v1.0.0` tells which version of the pipeline should be used (you can check the number of the latest version on the GitHub repository of the pipeline and change it accordingly)
+* `-r v1.X.X` tells which version of the pipeline should be used (you can check the number of the latest version on the GitHub repository of the pipeline and change it accordingly)
 
 * `-profile docker` this tells Nextflow which configuration profile it should use and you can find the available options on the GitHub repository. The pipeline currently includes profiles for [Docker](https://www.docker.com/) [Singularity](https://apptainer.org/) and [Slurm](https://slurm.schedmd.com/documentation.html). You can learn more about this [here](../configuration/profiles).
 

nextflow.config

@@ -1,7 +1,7 @@
 
 manifest {
     name                                  = 'nf-gwas'
-    version                               = '1.0.7'
+    version                               = '1.0.8'
     description                           = 'A Nextflow GWAS pipeline.'
     author                                = 'Lukas Forer and Sebastian Schönherr'
     homePage                              = 'https://github.com/genepi/nf-gwas'
@@ -115,7 +115,7 @@ params {
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
-process.container = 'quay.io/genepi/nf-gwas:v1.0.7'
+process.container = 'quay.io/genepi/nf-gwas:v1.0.8'
 
 profiles {
     debug { process.beforeScript          = 'echo $HOSTNAME' }