Circularmapper filter fix

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Removed leftover old DockerHub push CI commands.
 - [#627](https://github.com/nf-core/eager/issues/627) Added de Barros Damgaard citation to README
 - [#630](https://github.com/nf-core/eager/pull/630) Better handling of Qualimap memory requirements and error strategy.
+- [#638](https://github.com/nf-core/eager/issues/638#issuecomment-748877567) Fixed inverted circularfilter filtering (previously filtering would happen by default, not when requested by user as originally recorded in documentation)
 
 ### `Dependencies`
 

docs/usage.md

@@ -391,203 +391,6 @@ hard drive footprint of the run, so be sure to do this!
 
 ## Troubleshooting and FAQs
 
-### My pipeline update doesn't seem to do anything
-
-To download a new version of a pipeline, you can use the following, replacing
-`<VERSION>` to the corresponding version.
-
-```bash
-nextflow pull nf-core/eager -r <VERSION>
-```
-
-However, in very rare cases, minor fixes to a version will be pushed out without
-a version number bump. This can confuse nextflow slightly, as it thinks you
-already have the 'broken' version from your original pipeline download.
-
-If when running the pipeline you don't see any changes in the fixed version when
-running it, you can try removing your nextflow EAGER cache typically stored in
-your home directory with
-
-```bash
-rm -r ~/.nextflow/assets/nf-core/eager
-```
-
-And re-pull the pipeline with the command above. This will install a fresh
-version of the version with the fixes.
-
-### Input files not found
-
-When using the [direct input](#direct-input-method) method: if no file, only one
-input file, or only 'read one' and not 'read two' is picked up then something is
-likely wrong with your input file declaration ([`--input`](#--input)):
-
-1. The path must be enclosed in quotes (`'` or `"`)
-2. The path must have at least one `*` wildcard character. This is even if you
-   are only running one paired end sample.
-3. When using the pipeline with paired end data, the path must use `{1,2}` or
-   `{R1,R2}` notation to specify read pairs.
-4. If you are running single-end data make sure to specify `--single_end`
-
-**Important**: The pipeline can't take a list of multiple input files when using
-the direct input method - it takes a 'glob' expression. If your input files are
-scattered in different paths then we recommend that you generate a directory
-with symlinked files. If running in paired-end mode please make sure that your
-files are sensibly named so that they can be properly paired. See the previous
-point.
-
-If the pipeline can't find your files then you will get the following error
-
-```bash
-ERROR ~ Cannot find any reads matching: *{1,2}.fastq.gz
-```
-
-If your sample name is "messy" then you have to be very particular with your
-glob specification. A file name like `L1-1-D-2h_S1_L002_R1_001.fastq.gz` can be
-difficult enough for a human to read. Specifying `*{1,2}*.gz` won't work give
-you what you want whilst `*{R1,R2}*.gz` (i.e. the addition of the `R`s) will.
-
-If using the [TSV input](#tsv-input-method) method, this likely means there is a
-mistake or typo in the path in a given column. Often this is a trailing space at
-the end of the path.
-
-### I am only getting output for a single sample although I specified multiple with wildcards
-
-You must specify paths to files in quotes, otherwise your shell will evaluate
-any wildcards (\*) rather than Nextflow.
-
-For example
-
-```bash
-nextflow run nf-core/eager --input /path/to/sample_*/*.fq.gz
-```
-
-Would be evaluated by your shell as  
-
-```bash
-nextflow run nf-core/eager --input /path/to/sample_1/sample_1.fq.gz /path/to/sample_1/sample_1.fq.gz /path/to/sample_1/sample_1.fq.gz
-```
-
-And Nextflow will only take the first path after `--input`, ignoring the others.
-
-On the other hand, encapsulating the path in quotes will allow Nextflow to
-evaluate the paths.
-
-```bash
-nextflow run nf-core/eager --input "/path/to/sample_*/*.fq.gz"
-```
-
-### The pipeline crashes almost immediately with an early pipeline step
-
-Sometimes a newly downloaded and set up nf-core/eager pipeline will encounter an
-issue where a run almost immediately crashes (e.g. at `fastqc`,
-`output_documentation` etc.) saying the tool could not be found or similar.
-
-#### I am running Docker
-
-You may have an outdated container. This happens more often when running on the
-`dev` branch of nf-core/eager, because Docker will _not_ update the container on
-each new commit, and thus may not get new tools called within the pipeline code.
-
-To fix, just re-pull the nf-core/eager Docker container manually with:
-
-```bash
-docker pull nfcore/eager:dev
-```
-
-#### I am running Singularity
-
-If you're running Singularity, it could be that Nextflow cannot access your
-Singularity image properly - often due to missing bind paths.
-
-See
-[here](https://nf-co.re/usage/troubleshooting#cannot-find-input-files-when-using-singularity)
-for more information.
-
-### The pipeline has crashed with an error but Nextflow is still running
-
-If this happens, you can either wait until all other already running jobs to
-safely finish, or if Nextflow _still_ does not stop press `ctrl + c` on your
-keyboard (or equivalent) to stop the Nextflow run.
-
-> :warning: if you do this, and do not plan to fix the run make sure to delete
-the output folder. Otherwise you may end up a lot of large intermediate files
-being left! You can clean a Nextflow run of all intermediate files with
-`nextflow clean -f -k` or delete the `work/` directory.
-
-### I get a exceeded job memory limit error
-
-While Nextflow tries to make your life easier by automatically retrying jobs
-that run out of memory with more resources (until your specified max-limit),
-sometimes you may have such large data you run out even after the default 3
-retries.
-
-To fix this you need to change the default memory requirements for the process
-that is breaking. We can do this by making a custom profile, which we then
-provide to the Nextflow run command.
-
-For example, lets say it's the `markduplicates` process that is running out of
-memory.
-
-First we need to check to see what default memory value we have. We can do this
-by going to the main [nf-core/eager code](https://github.com/nf-core/) and
-opening the `main.nf` file. We can then use your browser's find functionality
-for: `process markduplicates`.
-
-Once found, we then need to check the line called `label`. In this case the
-label is `mc_small` (for multi-core small).
-
-Next we need to go back to the main github repository, and open
-`conf/base.config`. Again using our find functionality, we search for:
-`withLabel:'mc_small'`.
-
-We see that the `memory` is set to `4.GB` (`memory = { check_max( 4.GB *
-task.attempt, 'memory' )})`).
-
-Now back on your computer, we need to make a new file called
-`custom_resources.conf`. You should save it somewhere centrally so you can
-reuse it.
-
-> If you think this would be useful for multiple people in your lab/institute,
-> we highly recommend you make an institutional profile at
-> [nf-core/configs](https://github.com/nf-core/configs). This will simplify this
-> process in the future.
-
-Within this file, you will need to add the following:
-
-```txt
-profiles {
-    big_data {
-      process {
-        withName: markduplicates {
-          memory = 16.GB
-        }
-      }
-    }
-}
-```
-
-Where we have increased the default `4.GB` to `16.GB`. Make sure that you keep
-the `check_max` function, as this prevents your run asking for too much memory
-during retries.
-
-> Note that with this you will _not_ have the automatic retry mechanism. If
-> you want this, re-add the `check_max()` function on the `memory` line, and
-> add to the bottom of the entire file (outside the profiles block), the
-> block starting `def check_max(obj, type) {`, which is at the end of the
-> [nextflow.config file](https://github.com/nf-core/eager/blob/master/nextflow.config)
-
-Once saved, we can then modify your original Nextflow run command:
-
-```bash
-nextflow run nf-core/eager -r 2.2.0 -c /<path>/<to>/custom_resources.conf -profile big_data,<original>,<profiles> <...>
-```
-
-Where we have added `-c` to specify which file to use for the custom profiles,
-and then added the `big_data` profile to the original profiles you were using.
-
-:warning: it's important that big_data comes first, to ensure it overwrites any
-parameters set in the subsequent profiles!
-
 ### I get a file name collision error during merging
 
 When using TSV input, nf-core/eager will attempt to merge all `Lanes` of a
@@ -608,37 +411,6 @@ they are unique (e.g. if one library was sequenced on Lane 8 of two HiSeq runs,
 specify lanes as 8 and 16 for each FASTQ file respectively). For library merging
 errors, you must modify your `Library_ID`s accordingly, to make them unique.
 
-### I specified a module and it didn't produce the expected output
-
-Possible options:
-
-1. Check there if you have a typo in the parameter name. Nextflow _does not_
-   check for this
-2. Check that an upstream module was turned on (if a module requires the output
-   of a previous module, it will not be activated unless it receives the output)
-
-### I get a unable to acquire lock
-
-Errors like the following
-
-```bash
-Unable to acquire lock on session with ID 84333844-66e3-4846-a664-b446d070f775
-```
-
-normally suggest a previous Nextflow run (on the same folder) was not cleanly
-killed by a user (e.g. using ctrl + z to hard kill a crashed run).
-
-To fix this, you must clean the entirety of the output directory (including
-output files) e.g. with `rm -r <output_dir>/* <output_dir>/.*` and re-running
-from scratch.
-
-`ctrl +z` is **not** a recommended way of killing a Nextflow job. Runs that take
-a long time to fail are often still running because other job submissions are
-still running. Nextflow will normally wait for those processes to complete
-before cleaning shutting down the run (to allow rerunning of a run with
-`-resume`). `ctrl + c` is much safer as it will tell Nextflow to stop earlier
-but cleanly.
-
 ## Tutorials
 
 ### Tutorial - How to investigate a failed run

main.nf

@@ -87,7 +87,7 @@ def helpMessage() {
       --bwaalnl [num]            Specify the -l parameter for BWA aln, i.e. length of seeds to be used. Set to 1024 for whole read. Default: ${params.bwaalnl}
       --circularextension [num]  Specify the number of bases to extend reference by (circularmapper only). Default: ${params.circularextension}
       --circulartarget [chr]     Specify the FASTA header of the target chromosome to extend(circularmapper only). Default: '${params.circulartarget}'
-      --circularfilter [bool]    Turn on to filter off-target reads (circularmapper only).
+      --circularfilter [bool]    Turn on to remove reads that did not map to the circularised genome (circularmapper only).
       --bt2_alignmode [str]      Specify the bowtie2 alignment mode. Options:  'local', 'end-to-end'. Default: '${params.bt2_alignmode}'
       --bt2_sensitivity [str]    Specify the level of sensitivity for the bowtie2 alignment mode. Options: 'no-preset', 'very-fast', 'fast', 'sensitive', 'very-sensitive'. Default: '${params.bt2_sensitivity}'
       --bt2n [num]               Specify the -N parameter for bowtie2 (mismatches in seed). This will override defaults from alignmode/sensitivity. Default: ${params.bt2n}
@@ -1541,6 +1541,7 @@ process circulargenerator{
             else null
     }
 
+
     input:
     file fasta from ch_fasta_for_circulargenerator
 
@@ -1578,7 +1579,7 @@ process circularmapper{
     params.mapper == 'circularmapper'
 
     script:
-    def filter = params.circularfilter ? '' : '-f true -x false'
+    def filter = params.circularfilter ? '-f true -x false' : ''
     def elongated_root = "${fasta.baseName}_${params.circularextension}.fasta"
     def size = params.large_ref ? '-c' : ''
 

nextflow_schema.json

@@ -555,7 +555,7 @@
                 },
                 "circularfilter": {
                     "type": "boolean",
-                    "description": "Turn on to filter off-target reads (circularmapper only).",
+                    "description": "Turn on to remove reads that did not map to the circularised genome (circularmapper only).",
                     "fa_icon": "fas fa-filter",
                     "help_text": "If you want to filter out reads that don't map to a circular chromosome, turn this on. By default this option is turned off.\n"
                 },
@@ -1575,4 +1575,4 @@
             "$ref": "#/definitions/metagenomic_authentication"
         }
     ]
-}
+}