Update usage docs

Author: drpatelh

docs/usage.md

@@ -167,7 +167,7 @@ Please get in touch with us on the #rnaseq channel in the [nf-core Slack workspa
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/rnaseq --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker
+nextflow run nf-core/rnaseq --input <SAMPLESHEET> --outdir <OUTDIR> --genome GRCh37 -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -196,8 +196,8 @@ nextflow run nf-core/rnaseq -profile docker -params-file params.yaml
 with `params.yaml` containing:
 
 ```yaml
-input: './samplesheet.csv'
-outdir: './results/'
+input: <SAMPLESHEET>
+outdir: <OUTDIR>
 genome: 'GRCh37'
 <...>
 ```

modules.json

@@ -52,7 +52,7 @@
                     },
                     "hisat2/align": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["fastq_align_hisat2"]
                     },
                     "hisat2/build": {
@@ -82,12 +82,12 @@
                     },
                     "rsem/calculateexpression": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
                     "rsem/preparereference": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
                     "rseqc/bamstat": {
@@ -176,12 +176,12 @@
                     },
                     "star/align": {
                         "branch": "master",
-                        "git_sha": "140d5a0d014138524e21dea80588817ddfc5dcf4",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
                     "stringtie/stringtie": {