Merge pull request #1005 from mskcc/update/remove_pipeline_nf_docs

removed deprecated pipeline.nf mentions from docs

docs/juno-setup.md

@@ -53,10 +53,10 @@ The call `which java` should return `/opt/common/CentOS_7/java/jdk1.8.0_202/bin/
 You can run a the pipeline on small test files to ensure that you are ready to run real data. If you experience any issues, something in your environment might be the reason. The following should take approximately 30 minutes and all tasks should succeed at first attempt:
 
 ```shell
-nextflow run pipeline.nf \
-    --mapping test_inputs/local/full_test_mapping.tsv \ 
+nextflow run dsl2.nf \
+    --mapping test_inputs/local/full_test_mapping.tsv \
     --pairing test_inputs/local/full_test_pairing.tsv \
     -profile test_singularity \
     --outDir results
-    --somatic --germline --QC --aggregate
+    --aggregate
 ```

docs/nextflow-basics.md

@@ -12,4 +12,4 @@
 
 * __View intermediate output__: As the pipeline runs, everything needed to execute each process in the pipeline is located in the `work` in the run directory. Thus, you can peek at input and output files for each step of the pipeline in real time.
 
-* __Run or skip specific tools:__ `pipeline.nf` has the argument `--tools`, which allows users to run only certain bioinformatic tools and skip others. The `--somatic` and `--germline` flags already have a preset of tools to include during a run, but you can limit this further by providing the `--tools` flag, followed by a comma-delimited string. For example, to use only DELLY for your somatic/germline runs, do `--somatic --germline --tools delly`; to use MuTect2, Manta, and Strelka2, do `--somatic --tools mutect2,manta,strelka2`.
+* __Run or skip specific subworkflows:__ `dsl2.nf` has the argument `--workflows`, which allows users to run only certain bioinformatic subworkflows and skip others. By default, nextflow uses the following string to run all subworkflows: `'snv,sv,mutsig,lohhla,facets,qc,msisensor'`. You can limit the subworkflows by providing a comma-delimited string to `--workflows` containing only the workflows you want.

docs/reference-files.md

@@ -1,6 +1,6 @@
 # Reference Files
 
-This and associated pages in this section provide details on the provenance and generation of all reference files used in `pipeline.nf`. Usage of these files is defined in the [references configuration file](https://github.com/mskcc/tempo/blob/master/conf/references.config).
+This and associated pages in this section provide details on the provenance and generation of all reference files used in `dsl2.nf`. Usage of these files is defined in the [references configuration file](https://github.com/mskcc/tempo/blob/master/conf/references.config).
 
 ::: tip Note
 All reference files described herein are in assembly GRCh37/hg19 of the human genome.

docs/running-the-pipeline.md

@@ -6,7 +6,7 @@
 Tempo does not support running samples from mixed sequencing platforms together. By default, the pipeline assumes the inputs are from exome sequencing.
 :::
 
-This page provides instructions on how to run the pipeline through the `pipeline.nf` script. The basic command below shows how to run Tempo, with an explanation of flags and input arguments and files. Below is also described how to best [run the pipeline on Juno](running-the-pipeline.md#running-the-pipeline-on-juno) as well as [on AWS](running-the-pipeline.md#running-the-pipeline-on-aws).
+This page provides instructions on how to run the pipeline through the `dsl2.nf` script. The basic command below shows how to run Tempo, with an explanation of flags and input arguments and files. Below is also described how to best [run the pipeline on Juno](running-the-pipeline.md#running-the-pipeline-on-juno) as well as [on AWS](running-the-pipeline.md#running-the-pipeline-on-aws).
 
 
 ```shell

docs/troubleshooting.md

@@ -13,7 +13,7 @@ You can follow the Nextflow process by following what is printed to `stdout`. Ad
 
 A job running a single process inside the pipeline can fail due to inadequate resources, which will trigger a re-run with increased resources. For other failures, you need to look inside the `work` directory. In the `.html` reports generated by default (or the `trace.txt` file) in the run directory you will find for each process run its status (`COMPLETED`; `CACHED` if resumed and completed in a prior run; and `FAILED` if an error occured) and a `hash`. The hash indicates the subdirectory in which the process was run (for example `a4/00365e` points to `work/a4/00365e9190eca55907746edeb58f77`). In this directory you find the following files which are useful for troubleshooting:
 - `.command.run`: This is the actual script which sets environment variables and runs `.command.sh`, Nextflow submits this to LSF using bsub. You can manually resubmit it by running `bsub < .command.run`.
-- `.command.sh`: This contains the command-line calls that are defined in the corresponding process in `pipeline.nf`.
+- `.command.sh`: This contains the executable script generated by the process definition.
 - `.command.log`: Contains `stdout` from the process itself and `bsub`.
 - `.command.out`: `stdout` from the process.
 - `.command.err`: `stderr` from the process.

docs/variant-annotation-and-filtering.md

@@ -2,8 +2,9 @@
 
 :::tip Note
 Hard-coded filter thresholds are viewable and editable in the configuration files here:
-[* Exomes](../conf/exome.config)
-[* Genomes](../conf/genome.config)
+* [Exomes](https://github.com/mskcc/tempo/blob/develop/conf/exome.config)
+* [Genomes](https://github.com/mskcc/tempo/blob/develop/conf/genome.config)
+
 :::
 
 ::: warning Be aware