diff --git a/Modules/Align/bwa.md b/Modules/Align/bwa.md
index 65a6e3e88..34db2471a 100644
--- a/Modules/Align/bwa.md
+++ b/Modules/Align/bwa.md
@@ -18,10 +18,10 @@ such as those derived using `harpy qc`. You can map reads onto a genome assembly
 using the `align` module:
 
 ```bash usage
-harpy align bwa|ema OPTIONS...
+harpy align bwa OPTIONS... INPUTS...
 ```
 ```bash example
-harpy align bwa --genome genome.fasta --directory Sequences/ 
+harpy align bwa --genome genome.fasta Sequences/ 
 ```
 
 ## :icon-terminal: Running Options
@@ -29,8 +29,8 @@ In addition to the [common runtime options](/commonoptions.md), the `harpy align
 
 | argument           | short name | type                  | default | required | description                                           |
 |:-------------------|:----------:|:----------------------|:-------:|:--------:|:------------------------------------------------------|
+| `INPUTS`           |            | file/directory paths  |         | **yes**  | Files or directories containing [input FASTQ files](/commonoptions.md#input-arguments)     |
 | `--genome`         |    `-g`    | file path             |         | **yes**  | Genome assembly for read mapping                      |
-| `--directory`      |    `-d`    | folder path           |         | **yes**  | Directory with sample sequences                       |
 | `--molecule-distance` |    `-m`    | integer         |  100000  |    no    | Base-pair distance threshold to separate molecules      |
 | `--quality-filter` |    `-f`    | integer (0-40)        |   30    |    no    | Minimum `MQ` (SAM mapping quality) to pass filtering  |
 | `--method`         |    `-m`    | choice [`bwa`, `ema`] |   bwa   |    no    | Which aligning software to use                        |
@@ -44,7 +44,13 @@ to assign alignments a unique Molecular Identifier `MI:i` tag based on their
 what this value does. 
 
 ## Quality filtering
-==- What is a $MQ$ score?
+The `--quality` argument filters out alignments below a given $MQ$ threshold. The default, `30`, keeps alignments
+that are at least 99.9% likely correctly mapped. Set this value to `1` if you only want alignments removed with
+$MQ = 0$ (0% likely correct). You may also set it to `0` to keep all alignments for diagnostic purposes.
+The plot below shows the relationship between $MQ$ score and the likelihood the alignment is correct and will serve to help you decide
+on a value you may want to use. It is common to remove alignments with $MQ <30$ (<99.9% chance correct) or $MQ <40$ (<99.99% chance correct).
+
+==- What is the $MQ$ score?
 Every alignment in a BAM file has an associated mapping quality score ($MQ$) that informs you of the likelihood 
 that the alignment is accurate. This score can range from 0-40, where higher numbers mean the alignment is more
 likely correct. The math governing the $MQ$ score actually calculates the percent chance the alignment is ***incorrect***: 
@@ -58,14 +64,9 @@ $$
 \text{or} \\
 \%\ chance\ correct = (1 - 10^\frac{-MQ}{10}) \times 100
 $$
-===
-The `--quality` argument filters out alignments below a given $MQ$ threshold. The default, `30`, keeps alignments
-that are at least 99.9% likely correctly mapped. Set this value to `1` if you only want alignments removed with
-$MQ = 0$ (0% likely correct). You may also set it to `0` to keep all alignments for diagnostic purposes.
-The plot below shows the relationship between $MQ$ score and the likelihood the alignment is correct and will serve to help you decide
-on a value you may want to use. It is common to remove alignments with $MQ <30$ (<99.9% chance correct) or $MQ <40$ (<99.99% chance correct).
 
 [!embed el="embed"](//plotly.com/~pdimens/7.embed)
+===
 
 ## Marking PCR duplicates
 Harpy uses `samtools markdup` to mark putative PCR duplicates. By using the `--barcode-tag BX`
diff --git a/Modules/Align/ema.md b/Modules/Align/ema.md
index ad621ba9b..5877d6cf8 100644
--- a/Modules/Align/ema.md
+++ b/Modules/Align/ema.md
@@ -25,10 +25,10 @@ such as those derived using `harpy qc`. You can map reads onto a genome assembly
 using the `align` module:
 
 ```bash usage
-harpy align OPTIONS...
+harpy align ema OPTIONS... INPUTS...
 ```
 ```bash example
-harpy align ema --genome genome.fasta --directory Sequences/ 
+harpy align ema --genome genome.fasta Sequences/ 
 ```
 
 
@@ -37,10 +37,10 @@ In addition to the [common runtime options](/commonoptions.md), the `harpy align
 
 | argument           | short name | type                  | default | required | description                                                        |
 |:-------------------|:----------:|:----------------------|:-------:|:--------:|:-------------------------------------------------------------------|
+| `INPUTS`           |            | file/directory paths  |         | **yes**  | Files or directories containing [input FASTQ files](/commonoptions.md#input-arguments)                  |
 | `--genome`         |    `-g`    | file path             |         | **yes**  | Genome assembly for read mapping                                   |
 | `--platform`       |    `-p`    | string                | haplotag | **yes** | Linked read technology: `haplotag` or `10x`                        |
 | `--whitelist`      |    `-w`    | file path             |         |    no    | Path to barcode whitelist (`--platform 10x` only)                  |
-| `--directory`      |    `-d`    | folder path           |         | **yes**  | Directory with sample sequences                                    |
 | `--ema-bins`       |    `-e`    | integer (1-1000)      |   500   |    no    | Number of barcode bins for EMA                                     |
 | `--quality-filter` |    `-f`    | integer (0-40)        |   30    |    no    | Minimum `MQ` (SAM mapping quality) to pass filtering               |
 | `--extra-params`   |    `-x`    | string                |         |    no    | Additional EMA-align/BWA arguments, in quotes                      |
@@ -52,7 +52,13 @@ If you need to process 10x data, then you will need to include the whitelist fil
 Conveniently, **haplotag data doesn't require this file**.
 
 ## Quality filtering
-==- What is a $MQ$ score?
+The `--quality` argument filters out alignments below a given $MQ$ threshold. The default, `30`, keeps alignments
+that are at least 99.9% likely correctly mapped. Set this value to `1` if you only want alignments removed with
+$MQ = 0$ (0% likely correct). You may also set it to `0` to keep all alignments for diagnostic purposes.
+The plot below shows the relationship between $MQ$ score and the likelihood the alignment is correct and will serve to help you decide
+on a value you may want to use. It is common to remove alignments with $MQ <30$ (<99.9% chance correct) or $MQ <40$ (<99.99% chance correct).
+
+==- What is the $MQ$ score?
 Every alignment in a BAM file has an associated mapping quality score ($MQ$) that informs you of the likelihood 
 that the alignment is accurate. This score can range from 0-40, where higher numbers mean the alignment is more
 likely correct. The math governing the $MQ$ score actually calculates the percent chance the alignment is ***incorrect***: 
@@ -66,14 +72,9 @@ $$
 \text{or} \\
 \%\ chance\ correct = (1 - 10^\frac{-MQ}{10}) \times 100
 $$
-===
-The `--quality` argument filters out alignments below a given $MQ$ threshold. The default, `30`, keeps alignments
-that are at least 99.9% likely correctly mapped. Set this value to `1` if you only want alignments removed with
-$MQ = 0$ (0% likely correct). You may also set it to `0` to keep all alignments for diagnostic purposes.
-The plot below shows the relationship between $MQ$ score and the likelihood the alignment is correct and will serve to help you decide
-on a value you may want to use. It is common to remove alignments with $MQ <30$ (<99.9% chance correct) or $MQ <40$ (<99.99% chance correct).
 
 [!embed el="embed"](//plotly.com/~pdimens/7.embed)
+===
 
 ## Marking PCR duplicates
 EMA marks duplicates in the resulting alignments, however the read with invalid barcodes
diff --git a/Modules/SV/leviathan.md b/Modules/SV/leviathan.md
index c2a8e6548..181596b44 100644
--- a/Modules/SV/leviathan.md
+++ b/Modules/SV/leviathan.md
@@ -25,8 +25,8 @@ This file is optional and only useful if you want variant calling to happen on a
     - spaces can be used as delimeters too
 - the groups can be numbers or text (_i.e._ meaningful population names)
 - you can comment out lines with `#` for Harpy to ignore them
-- create with `harpy extra popgroup -d <samplefolder>` or manually
-- if created with `harpy extra popgroup`, all the samples will be assigned to group `pop1`
+- create with `harpy popgroup -d <samplefolder>` or manually
+- if created with `harpy popgroup`, all the samples will be assigned to group `pop1`
     - make sure to edit the second column to reflect your data correctly.
 
 ``` example file for --populations
@@ -47,16 +47,16 @@ from the sample names. A simple fix would be to use underscores (`_`) to differe
 
 After reads have been aligned, _e.g._ with `harpy align`, you can use those alignment files
 (`.bam`) to call structural variants in your data using LEVIATHAN. To make sure your data
-will work seemlessly with LEVIATHAN, the alignments in the input BAM files should **end**
+will work seemlessly with LEVIATHAN, the alignments in the [input BAM files](/commonoptions.md) should **end**
 with a `BX:Z:AxxCxxBxxDxx` tag. Use `harpy preflight bam` if you want to double-check file
 format validity.
 
 ```bash usage
-harpy sv leviathan OPTIONS... 
+harpy sv leviathan OPTIONS... INPUTS...
 ```
 
 ```bash example
-harpy sv leviathan --threads 20 --directory Align/bwa -g genome.fasta
+harpy sv leviathan --threads 20 -g genome.fasta Align/bwa
 ```
 
 ## :icon-terminal: Running Options
@@ -64,8 +64,8 @@ In addition to the [common runtime options](/commonoptions.md), the `harpy sv le
 
 | argument         | short name | type          | default | required | description                                        |
 |:-----------------|:----------:|:--------------|:-------:|:--------:|:---------------------------------------------------|
+| `INPUTS`         |            | file/directory paths  |         | **yes**  | Files or directories containing [input BAM files](/commonoptions.md#input-arguments)     |
 | `--genome`       |    `-g`    | file path     |         | **conditionally** | Genome assembly for phasing bam files     |
-| `--directory`    |    `-d`    | folder path   |         | **yes**           | Directory with sequence alignments                  |
 | `--populations`  |    `-p`    | file path     |         |    no             | Tab-delimited file of sample\<*tab*\>group         |
 | `--extra-params` |    `-x`    | string        |         |    no             | Additional naibr arguments, in quotes              |
 
diff --git a/Modules/SV/naibr.md b/Modules/SV/naibr.md
index 923ca85fc..4b8fa2d5d 100644
--- a/Modules/SV/naibr.md
+++ b/Modules/SV/naibr.md
@@ -20,8 +20,8 @@ This file is optional and only useful if you want variant calling to happen on a
     - spaces can be used as delimeters too
 - the groups can be numbers or text (_i.e._ meaningful population names)
 - you can comment out lines with `#` for Harpy to ignore them
-- create with `harpy extra popgroup -d <samplefolder>` or manually
-- if created with `harpy extra popgroup`, all the samples will be assigned to group `pop1`
+- create with `harpy popgroup -d <samplefolder>` or manually
+- if created with `harpy popgroup`, all the samples will be assigned to group `pop1`
     - make sure to edit the second column to reflect your data correctly.
 
 ``` example file for --populations
@@ -49,15 +49,15 @@ should already have that information (yay!). If your alignments don't have phasi
 then you will need to do a little extra work for NAIBR to work best with your data. This process is described below.
 
 ```bash usage
-harpy sv naibr OPTIONS... 
+harpy sv naibr OPTIONS... INPUTS...
 ```
 
 ```bash examples
 # input bams already phased
-harpy sv naibr --threads 20 --directory Align/bwa --genome genome.fasta
+harpy sv naibr --threads 20 --genome genome.fasta Align/bwa
 
 # input bams require phasing
-harpy sv naibr --threads 20 --directory Align/bwa --genome genome.fasta --vcf Variants/data.vcf.gz
+harpy sv naibr --threads 20 --genome genome.fasta --vcf Variants/data.vcf.gz Align/bwa
 ```
 
 ## :icon-terminal: Running Options
@@ -65,8 +65,8 @@ In addition to the [common runtime options](/commonoptions.md), the `harpy sv na
 
 | argument         | short name | type          | default | required | description                                        |
 |:-----------------|:----------:|:--------------|:-------:|:--------:|:---------------------------------------------------|
+| `INPUTS`         |            | file/directory paths  |         | **yes**  | Files or directories containing [input BAM files](/commonoptions.md#input-arguments)     |
 | `--genome`       |    `-g`    | file path     |         | **yes** | Genome assembly for phasing bam files     |
-| `--directory`    |    `-d`    | folder path   |         | **yes**           | Directory with sequence alignments                  |
 | `--vcf`          |    `-v`    | file path     |         | **conditionally** | Phased vcf file for phasing bam files     |
 | `--molecule-distance` |  `-m` | integer       |  100000 |    no             | Base-pair distance threshold to separate molecules |
 | `--populations`  |    `-p`    | file path     |         |    no             | Tab-delimited file of sample\<*tab*\>group         |
@@ -99,7 +99,7 @@ it too well.
 In order to get the best variant calling performance out of NAIBR, it requires _phased_ bam files as input. 
 The `--vcf` option is optional and not used by NAIBR. However, to use `harpy sv naibr` with
 bam files that are not phased, you will need to include `--vcf`, which Harpy uses with 
-`whatshap haplotag` to phase your input bam files prior to variant calling. See the [whatshap documentation](https://whatshap.readthedocs.io/en/latest/guide.html#whatshap-haplotag)
+`whatshap haplotag` to phase your input BAM files prior to variant calling. See the [whatshap documentation](https://whatshap.readthedocs.io/en/latest/guide.html#whatshap-haplotag)
 for more details on that process.
 
 #### a phased input --vcf
diff --git a/Modules/demultiplex.md b/Modules/demultiplex.md
index 124de2fd6..be96c822d 100644
--- a/Modules/demultiplex.md
+++ b/Modules/demultiplex.md
@@ -20,17 +20,17 @@ should have been added during the sample DNA preparation in a laboratory. The de
 haplotag technology you are using (read [Haplotag Types](#haplotag-types)).
 
 ```bash usage
-harpy demultiplex OPTIONS... 
+harpy demultiplex OPTIONS... INPUT
 ```
 ```bash example
-harpy demultiplex --threads 20 --file Plate_1_S001_R1.fastq.gz --samplesheet demux.schema
+harpy demultiplex --threads 20 --samplesheet demux.schema Plate_1_S001_R1.fastq.gz
 ```
 ## :icon-terminal: Running Options
 In addition to the [common runtime options](/commonoptions.md), the `harpy demultiplex` module is configured using these command-line arguments:
 
 | argument          | short name | type       | default | required | description                                                                          |
 |:------------------|:----------:|:-----------|:-------:|:--------:|:-------------------------------------------------------------------------------------|
-| `--file`          |    `-f`    | file path  |         | **yes**  | The forward (or reverse) multiplexed FASTQ file                                      |
+| `INPUT`           |            | file path  |         | **yes**  | The forward (or reverse) multiplexed FASTQ file                                      |
 | `--samplesheet`   |    `-b`    | file path  |         | **yes**  | Tab-delimited file of sample\<tab\>barcode                                           |
 | `--method`        |    `-m`    | choice     | `gen1`  | **yes**  | Haplotag technology of the sequences                                                 |
 
diff --git a/Modules/impute.md b/Modules/impute.md
index 8a6c0b8fb..f085d4d63 100644
--- a/Modules/impute.md
+++ b/Modules/impute.md
@@ -28,7 +28,7 @@ most from your data. Harpy uses `STITCH` to impute genotypes, a haplotype-based
 method that is linked-read aware. Imputing genotypes requires a variant call file 
 **containing SNPs**, such as that produced by `harpy variants`. You can impute genotypes with Harpy using the `impute` module:
 ```bash usage
-harpy impute OPTIONS...
+harpy impute OPTIONS... INPUTS...
 ```
 
 ```bash example
@@ -36,7 +36,7 @@ harpy impute OPTIONS...
 harpy stitchparams -o stitch.params 
 
 # run imputation
-harpy impute --threads 20 --vcf Variants/mpileup/variants.raw.bcf --directory Align/ema --parameters stitch.params
+harpy impute --threads 20 --vcf Variants/mpileup/variants.raw.bcf --parameters stitch.params Align/ema
 ```
 
 ## :icon-terminal: Running Options
@@ -44,8 +44,8 @@ In addition to the [common runtime options](/commonoptions.md), the `harpy imput
 
 | argument       | short name | type        |    default    | required | description                                                                                     |
 |:---------------|:----------:|:------------|:-------------:|:--------:|:------------------------------------------------------------------------------------------------|
+| `INPUTS`       |            | file/directory paths  |         | **yes**  | Files or directories containing [input BAM files](/commonoptions.md)     |
 | `--vcf`        |    `-v`    | file path   |               | **yes**  | Path to VCF/BCF file                                                                            |
-| `--directory`  |    `-d`    | folder path |               | **yes**  | Directory with sequence alignments                                                              |
 | `--extra-params` |  `-x`    | folder path |               |  no      | Extra arguments to add to the STITCH R function, provided in quotes and R syntax                |
 | `--vcf-samples`|            |    toggle   |               | no       | [Use samples present in vcf file](#prioritize-the-vcf-file) for imputation rather than those found the directory    |
 | `--parameters` |    `-p`    | file path   |               | **yes**  | STITCH [parameter file](#parameter-file) (tab-delimited)                                                           |
@@ -57,7 +57,7 @@ syntax (e.g. `regionStart=0`, `populations=c("GBA","CUE")`). The argument should
 however, if your additional parameters require the use of quotes (like the previous example), then wrap the `-x` argument 
 in **single quotes**. Otherwise, the format should take the form of `"arg1=value, arg2=value2"`. Example:
 ```bash
-harpy impute -v file.vcf -p stitch.params -t 15 -x 'regionStart=20, regionEnd=500'
+harpy impute -v file.vcf -p stitch.params -t 15 -x 'regionStart=20, regionEnd=500' Align/ema
 ```
 
 ### Prioritize the vcf file
@@ -227,7 +227,7 @@ Impute/
 |:------------------------------------|:--------------------------------------------------------------------------|
 | `logs/harpy.impute.log`             | relevant runtime parameters for the phase module                          |
 | `input/*.stitch`                    | biallelic SNPs used for imputation                                        |
-| `input/samples.list`                | list of input BAM files                                                   |
+| `input/samples.list`                | list of [input BAM files](/commonoptions.md)                                                   |
 | `input/samples.names`               | list of sample names                                                      |
 | `model*/concat.log`                 | output from bcftools concat to create final imputed bcf                   |
 | `model*/variants.imputed.bcf`       | final bcf file of imputed genotypes                                       |
diff --git a/Modules/othermodules.md b/Modules/othermodules.md
index 57115eb57..7cf014a48 100644
--- a/Modules/othermodules.md
+++ b/Modules/othermodules.md
@@ -18,9 +18,12 @@ The arguments represent different sub-commands and can be run in any order or co
 
 ### popgroup
 #### Sample grouping file for variant calling
+
+```bash
+harpy popgroup -o samples.groups data/
+```
 ##### arguments
 - `-o`, `--output`: name of the output file
-- `-d`, `--directory`: name of the directory of input files, either fastq or bam.
 
 This file is entirely optional and useful if you want SNP variant calling to happen on a
 per-population level via `harpy snp ... -p` or on samples pooled-as-populations via `harpy sv ... -p`.
diff --git a/Modules/phase.md b/Modules/phase.md
index 02afe144b..c29b8d13c 100644
--- a/Modules/phase.md
+++ b/Modules/phase.md
@@ -21,10 +21,10 @@ works on SNP data**, and will not work for structural variants produced by `LEVI
 phase genotypes into haplotypes with Harpy using the `phase` module:
 
 ```bash usage
-harpy phase OPTIONS... 
+harpy phase OPTIONS... INPUTS...
 ```
 ```bash example
-harpy phase --threads 20 --vcf Variants/variants.raw.bcf --directory Align/ema 
+harpy phase --threads 20 --vcf Variants/variants.raw.bcf Align/ema 
 ```
 
 ## :icon-terminal: Running Options
@@ -32,8 +32,8 @@ In addition to the [common runtime options](/commonoptions.md), the `harpy phase
 
 | argument              | short name | type            | default | required | description                                                          |
 |:----------------------|:----------:|:----------------|:-------:|:--------:|:---------------------------------------------------------------------|
+| `INPUTS`           |            | file/directory paths  |         | **yes**  | Files or directories containing [input BAM files](/commonoptions.md#input-arguments)     |
 | `--vcf`               |    `-v`    | file path       |         | **yes**  | Path to BCF/VCF file                                                 |
-| `--directory`         |    `-d`    | folder path     |         | **yes**  | Directory with sequence alignments                                   |
 | `--genome           ` |    `-g`    | file path       |         |    no    | Path to genome if wanting to also use reads spanning indels          |
 | `--molecule-distance` |    `-m`    | integer         |  100000  |    no    | Base-pair distance threshold to separate molecules                   |
 | `--prune-threshold`   |    `-p`    | integer (0-100) |    7    |    no    | PHRED-scale (%) threshold for pruning low-confidence SNPs            |
diff --git a/Modules/preflight.md b/Modules/preflight.md
index 6f053df82..4c98b45a7 100644
--- a/Modules/preflight.md
+++ b/Modules/preflight.md
@@ -27,17 +27,17 @@ for the pipeline. There are separate `fastq` and `bam` submodules and the result
 
 
 ```bash fastq usage and example
-harpy preflight fastq OPTIONS...
+harpy preflight fastq OPTIONS... INPUTS...
 
 # example 
-harpy preflight fastq --threads 20 -d raw_data
+harpy preflight fastq --threads 20 raw_data
 ```
 
 ```bash bam usage and example
-harpy preflight bam OPTIONS... 
+harpy preflight bam OPTIONS... INPUST...
 
 # example
-harpy preflight bam --threads 20 -d Align/bwa
+harpy preflight bam --threads 20 Align/bwa
 ```
 
 ## :icon-terminal: Running Options
@@ -45,12 +45,13 @@ In addition to the [common runtime options](/commonoptions.md), the `harpy prefl
 
 | argument          | short name | type       | default | required | description                                                                          |
 |:------------------|:----------:|:-----------|:-------:|:--------:|:-------------------------------------------------------------------------------------|
-| `--directory`          |    `-d`    | folder path |         | **yes**  | Directory with sequences or alignments                                                              |
+| `INPUTS`           |            | file/directory paths  |         | **yes**  | Files or directories containing [input fastq or bam files](/commonoptions.md#input-arguments)     |
 
 ## Workflow
 
 +++ `fastq` checks
-Below is a table of the format specifics `harpy preflight` checks for FASTQ files. Take note
+Below is a table of the format specifics `harpy preflight` checks for FASTQ files. Since 10X data doesn't use
+the haplotagging data format, you will find little value in running `preflight` on 10X FASTQ files. Take note
 of the language such as when "any" and "all" are written.
 
 | Criteria | Pass Condition | Fail Condition |
diff --git a/Modules/qc.md b/Modules/qc.md
index f52f92c6f..811792b1d 100644
--- a/Modules/qc.md
+++ b/Modules/qc.md
@@ -21,17 +21,17 @@ harpy qc OPTIONS...
 ```
 
 ```bash example
-harpy qc --directory Sequences_Raw/ --threads 20 
+harpy qc --threads 20 Sequences_Raw/ 
 ```
 
 ## :icon-terminal: Running Options
 In addition to the [common runtime options](/commonoptions.md), the `harpy qc` module is configured using these command-line arguments:
 
 | argument         | short name | type        | default | required | description                                                                                     |
-|:-----------------|:----------:|:------------|:-------:|:--------:|:------------------------------------------------------------------------------------------------|
-| `--directory`          |    `-d`    | folder path |         | **yes**  | Directory with sequence alignments                                                              |
-| `--max-length`   |    `-l`    | integer     |   150   |    no    | Maximum length to trim sequences down to                                                        |
-| `--extra-params` |    `-x`    | string      |         |    no    | Additional fastp arguments, in quotes                                                           |
+|:-----------------|:----------:|:------------|:-------:|:-------:|:------------------------------------------------------------------------------------------------|
+| `INPUTS`         |            | file/directory paths  |         | **yes**  | Files or directories containing [input FASTQ files](/commonoptions.md#input-arguments)     |
+| `--max-length`   |    `-l`    | integer     |   150   |    no   | Maximum length to trim sequences down to                                                        |
+| `--extra-params` |    `-x`    | string      |         |    no   | Additional fastp arguments, in quotes                                                           |
 
 ---
 ## :icon-git-pull-request: QC Workflow
diff --git a/Modules/snp.md b/Modules/snp.md
index 8a3c1495a..90e202ff6 100644
--- a/Modules/snp.md
+++ b/Modules/snp.md
@@ -11,15 +11,15 @@ order: 5
 - at least 4 cores/threads available
 - a genome assembly in FASTA format
 - sequence alignments, in `.bam` format
-- sample grouping file
+- sample grouping file (optional)
 ==- :icon-file: sample grouping file
 This file is optional and useful if you want variant calling to happen on a per-population level.
 - takes the format of sample\<*tab*\>group
     - spaces can be used as delimeters too
 - the groups can be numbers or text (_i.e._ meaningful population names)
 - you can comment out lines with `#` for Harpy to ignore them
-- create with `harpy extra popgroup -d <samplefolder>` or manually
-- if created with `harpy extra popgroup`, all the samples will be assigned to group `pop1`, so make sure to edit the second column to reflect your data correctly.
+- create with `harpy popgroup <samplefolder>` or manually
+- if created with `harpy popgroup`, all the samples will be assigned to group `pop1`, so make sure to edit the second column to reflect your data correctly.
 
 ``` example file for --populations
 sample1 pop1
@@ -43,15 +43,15 @@ After reads have been aligned, _e.g._, with `harpy align`, you can use those ali
 You can call SNPs with the ` harpy snp` module:
 
 ```bash usage
-harpy snp method OPTIONS... 
+harpy snp method OPTIONS... INPUTS...
 ```
 
 ```bash examples
 # call variants with mpileup
-harpy snp mpileup --threads 20 --genome genome.fasta --directory Align/bwa
+harpy snp mpileup --threads 20 --genome genome.fasta Align/bwa
 
 # call variants with freebayes
-harpy snp freebayes --threads 20 --genome genome.fasta --directory Align/bwa
+harpy snp freebayes --threads 20 --genome genome.fasta Align/bwa
 ```
 
 ## :icon-terminal: Running Options
@@ -59,8 +59,8 @@ In addition to the [common runtime options](../commonoptions.md), the `harpy snp
 
 | argument         | short name | type                            | default | required | description                                         |
 |:-----------------|:----------:|:--------------------------------|:-------:|:--------:|:----------------------------------------------------|
+| `INPUTS`           |            | file/directory paths  |         | **yes**  | Files or directories containing [input BAM files](/commonoptions.md#input-arguments)   |
 | `--genome`       |    `-g`    | file path                       |         | **yes**  | Genome assembly for variant calling                 |
-| `--directory`    |    `-d`    | folder path                     |         | **yes**  | Directory with sequence alignments                  |
 | `--windowsize`   |    `-w`    | integer                         |  50000  |    no    | Interval size for parallel variant calling          |
 | `--populations`  |    `-p`    | file path                       |         |    no    | Tab-delimited file of sample\<*tab*\>group            |
 | `--ploidy`       |    `-x`    | integer                         |    2    |    no    | Ploidy of samples                                   |
diff --git a/commonoptions.md b/commonoptions.md
index 5095e36e6..8b0744702 100644
--- a/commonoptions.md
+++ b/commonoptions.md
@@ -5,6 +5,35 @@ order: 4
 ---
 
 # :icon-list-unordered: Common Harpy Options
+## Input Arguments
+Each of the main Harpy modules (e.g. `qc` or `phase`) follows the format of
+```bash
+harpy module options arguments
+```
+where `module` is something like `impute` or `snp mpileup` and `options` are the runtime parameters,
+which can include things like an input `--vcf` file, `--molecule-distance`, etc. After the options
+is where you provide the input files/directories without flags and following standard BASH expansion
+rules (e.g. wildcards). You can mix and match entire directories, individual files, and wildcard expansions.
+In most cases, you can provide an unlimited amount of input arguments, which Harpy will parse and symlink
+into the `*/workflow/input` folder, leaving the original files unmodified. In practice, that can look like:
+```bash
+harpy align bwa -t 5 -g genome.fasta data/pop1 data/pop2/trimmed*gz data/pop3/sample{1,2}* data/pop4/sample{2..5}*gz 
+```
+!!!info not recursive
+Keep in mind that Harpy will not recursively scan input directories for files. If you provide `data/` as an input,
+Harpy will search for fastq/bam files in `data/` and not in any subdirectories within `data/`. This is done deliberately
+to avoid unexpected behavior.
+!!!
+
+!!!warning clashing names
+Harpy will symlink just the file names into `workflow/input` regardless of their origin,
+meaning that files in different directories that have the same name (ignoring extensions) will
+clash. As an example, both `folderA/sample001.bam` and `folderB/sample001.bam` will become symlinked
+as `workflow/input/sample001.bam`, with one symlink overwriting the other, leaving you with one missing
+sample. During parsing, Harpy will inform you of naming clashes and terminate to protect you against
+this behavior. 
+!!!
+
 ## Common command-line options
 Every Harpy module has a series of configuration parameters. These are arguments you need to input
 to configure the module to run on your data, such as the directory with the reads/alignments,
@@ -25,11 +54,11 @@ configured using these arguments:
 As as example, you could call the `harpy align` module and specify 20 threads with no output to console:
 
 ```bash
-harpy align bwa --threads 20 --directory samples/trimmedreads --quiet
+harpy align bwa --threads 20 --quiet samples/trimmedreads
 
-# same as #
+# identical to #
 
-harpy align bwa -t 20 -d samples/trimmedreads -q
+harpy align bwa -t 20 -q samples/trimmedreads
 ```
 ---
 
@@ -41,15 +70,15 @@ and the contents therein also allow you to rerun the workflow manually. The `wor
 
 | item | contents | utility |
 |:-----|:---------|:--------|
-|`*.smk`| Snakefile with the full recipe of the workflow | useful for understanding the workflow |
-| `config.yml` | Configuration file generated from command-line arguments and consumed by the Snakefile | useful for bookkeeping | 
-| `report/*.Rmd` | RMarkdown files used to generate the fancy reports | useful to understand math behind plots/tables or borrow code from |
+|`*.smk`               | Snakefile with the full recipe of the workflow | useful for understanding the workflow |
+| `config.yml`         | Configuration file generated from command-line arguments and consumed by the Snakefile | useful for bookkeeping | 
+| `input/`             | Symlinks to all of the provided input files with standardized extensions |
+| `report/*.Rmd`       | RMarkdown files used to generate the fancy reports | useful to understand math behind plots/tables or borrow code from |
 | `*.workflow.summary` | Plain-text overview of the important parts of the workflow | useful for bookkeeping and writing Methods |
 
 ---
 
 ## The `Genome` folder
-
 You will notice that many of the workflows will create a `Genome` folder in the working 
 directory. This folder is to make it easier for Harpy to store the genome and the associated
 indexing/etc. files. Your input genome will be symlinked into that directory (not copied), but
diff --git a/retype.yml b/retype.yml
index 2b447f94e..38383a029 100644
--- a/retype.yml
+++ b/retype.yml
@@ -16,15 +16,18 @@ links:
 footer:
   copyright: "&copy; Copyright {{ year }}. All rights reserved."
 branding:
-  title: Harpy           # Your custom website title; keep it short.
-  label: v0.6.1
-  logo: static/favicon.png          # Path to a logo file.
-  logoDark: static/favicon.png # Path to a logo file to use in dark mode.
+  title: Harpy
+  label: v0.7.0
+  logo: static/favicon.png
+  logoDark: static/favicon.png
   logoAlign: left
-favicon: static/favicon.png # Path to a custom favicon, or.
+favicon: static/favicon.png
 search:
   mode: partial
 edit:
   repo: "https://github.com/pdimens/HARPY/edit"
   base: /
   branch: "docs"
+exclude:
+  - "src/"
+  - "test/"
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